Linked .eps files cause error in InDesign CS5

I upgraded to CS5 about 2 weeks ago and all is well except:
In 2 files so far, some (but not all) of the links to .eps files (within anchored image frames) show up as gray rectangles with crossed diagonal lines. In addition, I get the following error message in a pop-up box:
"Error encountered while reading TIFF image. Image may be damaged or incompatible. Resave the image with different settings and try again."
I was able to make one graphic reappear correctly (at least for now) by opening the .eps file in AI CS3 (the latest I have), resaving it as a .ai file and doing a new Place. Is this the best way to resolve this issue for the several dozen .eps files? Or is there something else easier I should try?
Any ideas what's causing this issue? Is it maybe a known bug?
Thanks,
John
PS: The .eps files were created with 3rd party software (Sibelius music notation software), but I've never before (CS3 and CS4) had a problem.

I did NOT move the .eps files across a network (except that I have two computers in the same room and move files between them via an Ethernet hub in a Windows workgroup, but I assume you're referring to a LAN, which this is not).
Of course an Ethernet hub is a LAN! Absolutely! (LAN is a local area network.)
It's certainly a good idea to check to make sure the files are still the same, but if they still open in Illustrator, then they should work in InDesign.
(Moving files across networks, LANs or the Internet or what-have-you, should not corrupt them. But stranger things have happened.)
Also, you mention "tiny" PDFs...what? Generally speaking the PDFs should not be all that different in size from the eps files,
though it's possible for them to be both larger and smaller, depending. But why do you say "tiny"? I wonder if this may give us a hint about your problem.
Still, though, I wonder what I asked initially...can you boil this problem down to a small reproducible test case?

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Log 1:
Process:         Adobe InDesign CS5 [11565]
Path:            /Applications/Adobe InDesign CS5/Adobe InDesign CS5.app/Contents/MacOS/Adobe InDesign CS5
Identifier:      com.adobe.InDesign
Version:         7.0.4.553 (7040)
Code Type:       X86 (Native)
Parent Process: launchd [238]
User ID:         501
Date/Time:       2013-05-02 12:45:38.327 -0700
OS Version:      Mac OS X 10.8.2 (12C60)
Report Version: 10
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
Exception Type: EXC_BAD_ACCESS (SIGBUS)
Exception Codes: KERN_PROTECTION_FAILURE at 0x0000000000000004
VM Regions Near 0x4:
--> __PAGEZERO             0000000000000000-0000000000001000 [    4K] ---/--- SM=NUL /Applications/Adobe InDesign CS5/Adobe InDesign CS5.app/Contents/MacOS/Adobe InDesign CS5
    __TEXT                 0000000000001000-0000000000005000 [   16K] r-x/rwx SM=COW /Applications/Adobe InDesign CS5/Adobe InDesign CS5.app/Contents/MacOS/Adobe InDesign CS5
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   com.adobe.InDesign.Links                0x11da9cfd 0x11d39000 + 462077
1   com.adobe.InDesign.Links                0x11dad857 0x11d39000 + 477271
2   com.adobe.InDesign.Links                0x11dabcc0 0x11d39000 + 470208
3   com.adobe.InDesign.Links                0x11da96b9 0x11d39000 + 460473
4   DataBaseLib.dylib                       0x010fd89f InterfaceSnapshot::ResetObjectToSnapshot(IDataBase*, IPMUnknown*, IDType<SnapshotID_tag>, ISnapshotCache*, scoped_lastrevinfodataref&) + 575
5   ObjectModelLib.dylib                    0x01063b80 0x1038000 + 179072
6   ObjectModelLib.dylib                    0x01070eb8 ShuksanInit(IStartupScreen* (*)(), IPlugIn*) + 23784
7   DataBaseLib.dylib                       0x010ce158 0x10c9000 + 20824
8   com.adobe.InDesign.Links                0x11d7b093 0x11d39000 + 270483
9   com.adobe.InDesign.Links                0x11d7d991 0x11d39000 + 280977
10 com.adobe.InDesign.Links                0x11d8ee5a 0x11d39000 + 351834
11 com.adobe.InDesign.Links                0x11d9f17f 0x11d39000 + 418175
12 com.adobe.InDesign.Links                0x11da016e 0x11d39000 + 422254
13 com.adobe.InDesign.Links                0x11d78258 0x11d39000 + 258648
14 com.adobe.InDesign.Links                0x11e05bbc GetPlugIn + 191420
15 com.adobe.InDesign.Links                0x11e05836 GetPlugIn + 190518
16 com.adobe.InDesign.Document Framework          0x0d937a85 0xd936000 + 6789
17 com.adobe.InDesign.Document Framework          0x0d937b75 0xd936000 + 7029
18 com.adobe.InDesign.AppFramework          0x0bbb60ed GetPlugIn + 201661
19 com.adobe.InDesign.Links                0x11d71025 0x11d39000 + 229413
20 com.adobe.InDesign.Links                0x11d70d6c 0x11d39000 + 228716
21 ObjectModelLib.dylib                    0x01062640 0x1038000 + 173632
22 ObjectModelLib.dylib                    0x010651bb 0x1038000 + 184763
23 com.adobe.InDesign.Document Framework          0x0d9d0ed0 0xd936000 + 634576
24 com.adobe.InDesign.Links                0x11dc53f8 0x11d39000 + 574456
25 com.adobe.InDesign.Document Framework          0x0d937a85 0xd936000 + 6789
26 com.adobe.InDesign.Document Framework          0x0d937b75 0xd936000 + 7029
27 com.adobe.InDesign.AppFramework          0x0bbb60ed GetPlugIn + 201661
28 PublicLib.dylib                         0x01161d6c UIDList::ReadWrite(IPMStream*, UIDList::EXferType) + 204
29 PublicLib.dylib                         0x01161f50 UIDList::ReadWriteXferReference(IPMStream*) + 32
30 com.adobe.InDesign.Links                0x11db2d49 0x11d39000 + 499017
31 ObjectModelLib.dylib                    0x01062640 0x1038000 + 173632
32 ObjectModelLib.dylib                    0x01065ab5 0x1038000 + 187061
33 com.adobe.InDesign.Document Framework          0x0d9d13ec 0xd936000 + 635884
34 com.adobe.InDesign.Document Framework          0x0d9d0c1e 0xd936000 + 633886
35 com.adobe.InDesign.Generic Page Item          0x117a0a86 GetPlugIn + 149142
36 PublicLib.dylib                         0x01164422 Command::DoImmediate(short) + 34
37 com.adobe.InDesign.Utilities            0x0ce10aa3 0xce0f000 + 6819
38 com.adobe.InDesign.Utilities            0x0ce10ccc 0xce0f000 + 7372
39 com.adobe.InDesign.AppFramework          0x0bb7a688 0xbb60000 + 108168
40 PublicLib.dylib                         0x0116557b CmdUtils::ProcessCommand(ICommand*) + 59
41 com.adobe.InDesign.Document Framework          0x0d952c6d 0xd936000 + 117869
42 PublicLib.dylib                         0x01164422 Command::DoImmediate(short) + 34
43 com.adobe.InDesign.Utilities            0x0ce10aa3 0xce0f000 + 6819
44 com.adobe.InDesign.Utilities            0x0ce10ccc 0xce0f000 + 7372
45 com.adobe.InDesign.AppFramework          0x0bb7a688 0xbb60000 + 108168
46 PublicLib.dylib                         0x0116557b CmdUtils::ProcessCommand(ICommand*) + 59
47 PublicLib.dylib                         0x01163cd1 CompoundSequenceCmd::Do() + 369
48 PublicLib.dylib                         0x01164422 Command::DoImmediate(short) + 34
49 com.adobe.InDesign.Utilities            0x0ce10aa3 0xce0f000 + 6819
50 com.adobe.InDesign.Utilities            0x0ce10ccc 0xce0f000 + 7372
51 com.adobe.InDesign.AppFramework          0x0bb7a688 0xbb60000 + 108168
52 PublicLib.dylib                         0x0116557b CmdUtils::ProcessCommand(ICommand*) + 59
53 com.adobe.InDesign.AppFramework          0x0bb83bef 0xbb60000 + 146415
54 PublicLib.dylib                         0x01164422 Command::DoImmediate(short) + 34
55 com.adobe.InDesign.Utilities            0x0ce10aa3 0xce0f000 + 6819
56 com.adobe.InDesign.Utilities            0x0ce10ccc 0xce0f000 + 7372
57 com.adobe.InDesign.AppFramework          0x0bb7a688 0xbb60000 + 108168
58 PublicLib.dylib                         0x0116557b CmdUtils::ProcessCommand(ICommand*) + 59
59 com.adobe.InDesign.AppFramework          0x0bb83bef 0xbb60000 + 146415
60 PublicLib.dylib                         0x01164422 Command::DoImmediate(short) + 34
61 com.adobe.InDesign.Utilities            0x0ce10aa3 0xce0f000 + 6819
62 com.adobe.InDesign.Utilities            0x0ce10ccc 0xce0f000 + 7372
63 com.adobe.InDesign.AppFramework          0x0bb7a688 0xbb60000 + 108168
64 PublicLib.dylib                         0x0116557b CmdUtils::ProcessCommand(ICommand*) + 59
65 com.adobe.InDesign.Widgets              0x0e99304b GetPlugIn + 211323
66 com.adobe.InDesign.Widgets              0x0e996386 GetPlugIn + 224438
67 com.adobe.InDesign.Widgets              0x0e995fc0 GetPlugIn + 223472
68 PublicLib.dylib                         0x0117982b CScrapSuite_Extensible::Paste(IClipboardController*, IControlView*, short) + 219
69 com.adobe.InDesign.Application UI          0x0d3d1ff4 0xd3af000 + 143348
70 com.adobe.InDesign.Application UI          0x0d3d2f05 0xd3af000 + 147205
71 com.adobe.InDesign.Application UI          0x0d3d0abc 0xd3af000 + 137916
72 com.adobe.InDesign.Application UI          0x0d433632 GetPlugIn + 217730
73 com.adobe.InDesign.Actions              0x13d30de3 GetPlugIn + 11699
74 com.adobe.InDesign.Actions              0x13d1eccc 0x13d1d000 + 7372
75 WidgetBinLib.dylib                      0x02880334 MDefaultEH::KeyboardShortcut(IEvent*) + 484
76 WidgetBinLib.dylib                      0x0287fb34 CDefaultEH::KeyDown(IEvent*) + 148
77 WidgetBinLib.dylib                      0x02880133 MDefaultEH::KeyDown(IEvent*) + 163
78 PublicLib.dylib                         0x01184bee CEventDispatcher::DispatchToEventHandlers(IEvent*) + 222
79 PublicLib.dylib                         0x011846a8 CEventDispatcher::DispatchEvent(IEvent*, IEvent::SystemHandledState) + 24
80 com.adobe.InDesign.Application UI          0x0d446b99 GetPlugIn + 296937
81 com.adobe.InDesign.Application UI          0x0d4445dc GetPlugIn + 287276
82 com.apple.HIToolbox                     0x9995cb6b _InvokeEventHandlerUPP(OpaqueEventHandlerCallRef*, OpaqueEventRef*, void*, long (*)(OpaqueEventHandlerCallRef*, OpaqueEventRef*, void*)) + 36
83 com.apple.HIToolbox                     0x997e4594 DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*) + 1343
84 com.apple.HIToolbox                     0x997e3980 SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*, HandlerCallRec*) + 430
85 com.apple.HIToolbox                     0x997f7855 SendEventToEventTarget + 88
86 com.apple.HIToolbox                     0x998178b2 ToolboxEventDispatcherHandler(OpaqueEventHandlerCallRef*, OpaqueEventRef*, void*) + 2392
87 com.apple.HIToolbox                     0x997e4a3f DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*) + 2538
88 com.apple.HIToolbox                     0x997e3980 SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*, HandlerCallRec*) + 430
89 com.apple.HIToolbox                     0x997f7855 SendEventToEventTarget + 88
90 com.apple.HIToolbox                     0x997d9077 SendTSMEvent + 75
91 com.apple.HIToolbox                     0x997d8b0b SendUnicodeTextAEToUnicodeDoc + 745
92 com.apple.HIToolbox                     0x997d8704 TSMKeyEvent + 980
93 com.apple.HIToolbox                     0x998281e5 TSMProcessRawKeyEvent + 3102
94 com.apple.HIToolbox                     0x99868ec5 HandleCompatibilityKeyEvent + 323
95 com.apple.HIToolbox                     0x997e0aba HIApplication::EventHandler(OpaqueEventHandlerCallRef*, OpaqueEventRef*, void*) + 7318
96 com.apple.HIToolbox                     0x9995cb6b _InvokeEventHandlerUPP(OpaqueEventHandlerCallRef*, OpaqueEventRef*, void*, long (*)(OpaqueEventHandlerCallRef*, OpaqueEventRef*, void*)) + 36
97 com.apple.HIToolbox                     0x997e4594 DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*) + 1343
98 com.apple.HIToolbox                     0x997e3980 SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*, HandlerCallRec*) + 430
99 com.apple.HIToolbox                     0x997e37ca SendEventToEventTargetWithOptions + 94
100 com.apple.HIToolbox                     0x9981738c ToolboxEventDispatcherHandler(OpaqueEventHandlerCallRef*, OpaqueEventRef*, void*) + 1074
101 com.apple.HIToolbox                     0x997e4a3f DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*) + 2538
102 com.apple.HIToolbox                     0x997e3980 SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*, HandlerCallRec*) + 430
103 com.apple.HIToolbox                     0x997f7855 SendEventToEventTarget + 88
104 com.adobe.InDesign.AppFramework          0x0bb62fd5 0xbb60000 + 12245
105 com.adobe.InDesign.AppFramework          0x0bb884fa GetPlugIn + 14282
106 com.adobe.InDesign                      0x0000288b main + 187
107 com.adobe.InDesign                      0x000027a6 start + 54
Log 2:
Process:         Adobe InDesign CS5 [745]
Path:            /Applications/Adobe InDesign CS5/Adobe InDesign CS5.app/Contents/MacOS/Adobe InDesign CS5
Identifier:      com.adobe.InDesign
Version:         7.0.4.553 (7040)
Code Type:       X86 (Native)
Parent Process: launchd [142]
User ID:         501
Date/Time:       2013-05-07 15:00:42.593 -0700
OS Version:      Mac OS X 10.8.2 (12C60)
Report Version: 10
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
Exception Type: EXC_BAD_ACCESS (SIGBUS)
Exception Codes: KERN_PROTECTION_FAILURE at 0x0000000000000000
VM Regions Near 0:
--> __PAGEZERO             0000000000000000-0000000000001000 [    4K] ---/--- SM=NUL /Applications/Adobe InDesign CS5/Adobe InDesign CS5.app/Contents/MacOS/Adobe InDesign CS5
    __TEXT                 0000000000001000-0000000000005000 [   16K] r-x/rwx SM=COW /Applications/Adobe InDesign CS5/Adobe InDesign CS5.app/Contents/MacOS/Adobe InDesign CS5
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   com.adobe.InDesign.Text                 0x0ff26f59 GetPlugIn + 1072585
1   com.adobe.InDesign.Text                 0x0ff2c0eb GetPlugIn + 1093467
2   com.adobe.InDesign.Text                 0x0ff2c1ef GetPlugIn + 1093727
3   com.adobe.InDesign.Text                 0x0ff2c2c7 GetPlugIn + 1093943
4   DataBaseLib.dylib                       0x010fd89f InterfaceSnapshot::ResetObjectToSnapshot(IDataBase*, IPMUnknown*, IDType<SnapshotID_tag>, ISnapshotCache*, scoped_lastrevinfodataref&) + 575
5   ObjectModelLib.dylib                    0x01063b80 0x1038000 + 179072
6   ObjectModelLib.dylib                    0x01070eb8 ShuksanInit(IStartupScreen* (*)(), IPlugIn*) + 23784
7   DataBaseLib.dylib                       0x010ce158 0x10c9000 + 20824
8   com.adobe.InDesign.Text                 0x0ff2e909 GetPlugIn + 1103737
9   com.adobe.InDesign.Text                 0x1004932e GetPlugIn + 2261406
10 com.adobe.InDesign.Text                 0x0fe3fcba GetPlugIn + 125738
11 com.adobe.InDesign.Text                 0x0fe400ff GetPlugIn + 126831
12 com.adobe.InDesign.Text                 0x0fec3876 GetPlugIn + 665318
13 PublicLib.dylib                         0x01164422 Command::DoImmediate(short) + 34
14 com.adobe.InDesign.Utilities            0x0ce3baa3 0xce3a000 + 6819
15 com.adobe.InDesign.Utilities            0x0ce3bccc 0xce3a000 + 7372
16 com.adobe.InDesign.AppFramework          0x0bb7a688 0xbb60000 + 108168
17 com.adobe.InDesign.AppFramework          0x0bb6cf11 0xbb60000 + 53009
18 com.adobe.InDesign.AppFramework          0x0bb62f0e 0xbb60000 + 12046
19 com.adobe.InDesign.AppFramework          0x0bb884fa GetPlugIn + 14282
20 com.adobe.InDesign                      0x0000288b main + 187
21 com.adobe.InDesign                      0x000027a6 start + 54

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The "link related" and "text related" crashes were what I interpretted here, too, though I'm at a loss on how to proceed given that this is a fresh system and applications. This is happening with multiple InDesign projects in a design office environment where many others work on the same files and none of the other computers are having problems with these files. I've removed the same files listed (thank you for those) before and did so effectively with creating the new user account to test with, but it had no effect. I just tried again though, as these files could easily have becone corrupt again if they were being written to when InDesign crashed. Will let you know if that makes any difference. I've also gone through and completely cleaned out the fonts again and once more cleared the font caches. If need be I'll reboot this system into safe mode and try that way.
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          FROM   NO_SYS_USER_OBJECT_HISTORY
          WHERE USER_ID=UPPER($1)
          ORDER BY DATE_TIME DESC) H2
WHERE ROWNUM <= $2
    AND H1.AUTOID = H2.AUTOID)">
<method>
<ejb-name>NoUserHistoryEntry</ejb-name>
<method-name>findOldest</method-name>
<method-params>
   <method-param>java.lang.String</method-param>
   <method-param>java.lang.Integer</method-param>
</method-params>
</method>
</finder-method>
After deploying in 9.0.3 the following information is added to the orion-ejb-jar.xml file:
<finder-method query=
"NO_SYS_USER_OBJECT_HISTORY.USER_ID=UPPER($1) and
NO_SYS_USER_OBJECT_HISTORY.AUTOID NOT IN(
SELECT H1.AUTOID
FROM   NO_SYS_USER_OBJECT_HISTORY H1,
         (SELECT AUTOID
          FROM   NO_SYS_USER_OBJECT_HISTORY
          WHERE USER_ID=$1
          ORDER BY DATE_TIME DESC) H2
WHERE ROWNUM <= $2
    AND H1.AUTOID = H2.AUTOID)">

<method>
<ejb-name>NoUserHistoryEntry</ejb-name>
<method-name>findOldest</method-name>
<method-params>
   <method-param>java.lang.String</method-param>
   <method-param>java.lang.Integer</method-param>
</method-params>
</method>
</finder-method>
After deploying in 10.1.2.0.2 the following information is added to the
orion-ejb-jar.xml file:
<finder-method query=
"NO_SYS_USER_OBJECT_HISTORY.USER_ID=UPPER($1) and
NO_SYS_USER_OBJECT_HISTORY.AUTOID NOT IN(
SELECT H1.AUTOID
FROM   NO_SYS_USER_OBJECT_HISTORY H1,
         (SELECT AUTOID
          FROM   NO_SYS_USER_OBJECT_HISTORY
          WHERE USER_ID=UPPER($1)
          ORDER BY DATE_TIME DESC) H2
WHERE ROWNUM <= $2
    AND H1.AUTOID = H2.AUTOID)">


<method>
<ejb-name>NoUserHistoryEntry</ejb-name>
<method-name>findOldest</method-name>
<method-params>
   <method-param>java.lang.String</method-param>
   <method-param>java.lang.Integer</method-param>
</method-params>
</method>
</finder-method>
The problem with the 10.1.2.0.2 generated finders is that it is prepending H1 when
it should be NO_SYS_USER_OBJECT_HISTORY which results in the following error:
Exception in thread "main" com.cdtelecom.vygroe.configuration.ConfigurationException:
com.evermind.server.rmi.OrionRemoteException:
Transaction was rolled back: Database error: java.sql.SQLException:
ORA-00904: "H1"."SITE_DESCRIPTION": invalid identifier
; nested exception is:
        java.sql.SQLException: ORA-00904: "H1"."SITE_DESCRIPTION": invalid identifier
        at com.cdtelecom.vygroe.configuration.ConfigurationSession.internalRecordAction(ConfigurationSession.java:869)
        at com.cdtelecom.vygroe.configuration.ConfigurationSession.recordAction(ConfigurationSession.java:401)
        at com.cdtelecom.vygroe.configuration.Configuration.recordActionSaveOrder(Configuration.java:886)
        at com.cdtelecom.vygroe.configuration.Configuration.getOrder(Configuration.java:239)
        at test10g.main(test10g.java:47)
I tried to manually edit the file but when I shutdown and restart oc4j it regenerates the file again.

Jingzhi -- If you define the correct EJB-QL you should get the correct SQL generated for the finder. If that's not happening can you verify it against the OC4J v903 production release and see if it is still happening. I don't know if this helps with the JDeveloper problem specifically but if you don't need to create your own finders then that I hope should help.
Thanks -- Jeff

Linked PDF files cause Safari to crash

OsX 10.4.10 / Acrobat Professional 7...
When I click on a link in a web page that is a link to a PDF file, Acrobat 7 automatically starts up and then it and Safari crash once the Acrobat splash screen has run through its process.
Sometimes I am unaware that a link is to a PDF file so I cannot prevent this from happening by right/ctrl clicking to download the linked file.
I would like Safari set so it does not try to load PDF's within the browser (I'm assuming that's what's going on). I have checked the prefs. in Acrobat but they appear to be set so that it doesn't try to launch linked PDF's within Safari.
I did not have this problem when I was running OsX 10.3.9 not so long ago.
Any tips on how to fix/stop this from happening?
Christo

Does that mean Preview will open a PDF within Safari or does Safari automatically download the PDF first?
I would rather just download PDF's, when required, to view later.
Yes, that would open the PDF in Safari via Preview. If you want to skip Safari altogether, here's one suggestion for doing so. You'll need to use Terminal found in your Utilities folder.

Indesign cs5.5 out of memory error

Hi,
I am having constant problems with out of memory errors in indesign cs5.5 (version 7.5.3). I am on a mac. Everything is up to date, I have preflight off, my display performance is on typical view and have tried restarted my computer multiple times. I do not have any other programs open and the document I have open is 3 pages (8.5x11) with little content and a couple links to small images. I do not know what to do! This is affecting my job and my performance!! Please help!!! Thank you!

close the application
Rename the preferences from the following location
/Users/[User Name]/Library/Preferences/Adobe InDesign/Version #
/Users/[User Name]/Library/Caches/Adobe InDesign/Version [#]
then open a new document and then open the document you are facing an issue with it should clear the memory issue temporally
Alternate :
copy and paste the content in a new document and check if the 1st option does not work
PS : changing the folder name would reset the preferences
refer to KB : InDesign preferences and support file locations

InDesign CS4 Splitting colors from EPS file

I have CS4 and use illustrator to create logos, which I convert to eps files and place in InDesign. When I place the eps file into InDesign, sometimes, it splits the color of the EPS file down the middle and creates a light side and a dark side. Sometimes, this prints ok and other times, it prints with the split colors (light/dark). I have tried re-creating the logo file, recreating the inDesign file and nothing works. There is nothing showing behind the logo box in the InDesign file. I even had someone else convert the logo in CS5 and the same think happened. Does anyone have a clue as to what might be going on here? Any advice would be helpful.

1Karina wrote:
I am not sure I know what you mean. But eps does not work in InDesign, SRiegel is right, make it an ai file. Do you know you can copy the illustrator file and place it in InDesign? Or you can check the colours in the seperation box. Maybe you can see what is happening.
Actually, SOME .eps files can be problematic, but there's no blanket reason not to try them if you already have them. For new work, or for files that show a problem, saving as .ai or PDF is the way to go.

Linking Photoshop EPS Files with Clipping Paths

I'm running InDesign CS4 6.0.3 on a dual 2GHz G5 with Mac OS X 10.5.7.
We have a workflow that involves Photoshop EPS files being placed in InDesign with the object's clipping path set to Photoshop Path. If the link is updated or relinked, InDesign no longer restricts the image to the boundaries of the path—either on screen or on export to PDF—even though choosing Object -> Clipping Path -> Options still shows the type set to Photoshop Path. The only way that I have found to get the clipping path to fully apply to the image is to change the type from Photoshop Path to None and back to Photoshop Path, all while the Preview check box is on. I tried different combinations of turning the Apply Photoshop Clipping Path option on and off at the time of initial placement and at the time of relinking with no effect on this behavior.
Assuming that using a format other than EPS and using transparency rather than clipping paths are not in play at the moment, my questions are:
1. Is this a know issue with InDesign CS4? If so, can we expect a fix soon?
2. Is there anything that can be done on the user side that is less cumbersome than the workaround described above?

@Mark
Photoshop PSD is fine for all raster work. But if you have vector masks, vector shapes or text in the file then saving as PDF would be the better option, you can choose to remove the white background when importing the PDF in the Show Options of the Place Dialog box.
And that's null point anyway, as soon as you open a photoshop EPS file in Photoshop it rasterises everything. So what I said isn't a viable solution for this project. But to keep in mind that PSD will output as raster only and PDF can have transparency and raster + vector data.
Just thought I'd through that out there.

Linked .eps files cause error in InDesign CS5

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