Flash Builder Hangs when compiling to AIR App

I created a presentation in Catalyst with some embedded objects and some linked objects, then jumped it to Flash Builder to have my developer add in some scripts. We then tried to Export Release Build to create an AIR application. Problem is, it won't pull the linked assets. If I check the box to include the assets it hangs on the compilation. I can just keep clicking the "Finish" button and nothing happens. If I deselect the "Assets" I can click "Finish" it compiles the AIR application, but I'm left with a basically empty application. I don't understand what's happening. Any help please.
Thanks
Jim

Well Anirudh, it somewhat worked. I added the new source
folder just like you diagrammed and when I compiled the project to an AIR application the application file size jumped from 3mb to 500mb. So it obviously pulled the linked images. But when we installed the AIR application the images still weren't found. Any ideas?
Right now there are two items in the project that have Assets in the name. I don't think this is correct.
Here's a screen grab.

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    it() [0x33b3f000]
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    vent(EventManager.java:393)
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    r$EventThread)
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    va:332)
            at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.jav
    a:493)
            at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:149)
            at com.adobe.flexbuilder.standalone.FlexBuilderApplication.start(FlexBui
    lderApplication.java:109)
            at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandl
    e.java:194)
            at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runAppli
    cation(EclipseAppLauncher.java:110)
            at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(Ec
    lipseAppLauncher.java:79)
            at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.ja
    va:368)
            at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.ja
    va:179)
            at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
            at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
            at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
            at java.lang.reflect.Method.invoke(Unknown Source)
            at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:559)
            at org.eclipse.equinox.launcher.Main.basicRun(Main.java:514)
            at org.eclipse.equinox.launcher.Main.run(Main.java:1311)
    "VM Thread" prio=10 tid=0x32d40400 nid=0x254 runnable
    "VM Periodic Task Thread" prio=10 tid=0x32d62c00 nid=0xe48 waiting on condition
    JNI global references: 1690

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    faultDetail="Channel.Connect.Failed error
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    page_one had movieclip spread_one
    page_two had movieclip spread_two
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    on frame 1, (label page_one):
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    stop();
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              gotoAndStop("page_three");
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        at flash.display::MovieClip/gotoAndStop()
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    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:33:39.431
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:33:39.431
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:33:40.481
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:33:40.481
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:33:42.352
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:33:42.352
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:33:43.402
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:33:43.402
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:33:44.403
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:33:44.403
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:33:45.405
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:33:45.405
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:33:46.455
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:33:46.455
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:33:47.456
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:33:47.456
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:33:48.506
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:33:48.506
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:33:49.556
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:33:49.556
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:33:50.577
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:33:50.577
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:33:51.627
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:33:51.627
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:33:52.677
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:33:52.677
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:33:53.728
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:33:53.728
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:33:54.778
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:33:54.778
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:33:55.828
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:33:55.828
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:33:56.829
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:33:56.829
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:33:57.879
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:33:57.879
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:33:58.930
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:33:58.930
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:33:59.981
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:33:59.981
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:01.034
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:01.034
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:02.085
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:02.085
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:03.135
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:03.135
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:04.185
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:04.185
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:05.236
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:05.236
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:06.286
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:06.286
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:07.287
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:07.287
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:08.339
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:08.339
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:09.372
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:09.372
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:10.423
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:10.423
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:11.474
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:11.474
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:12.525
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:12.525
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:13.591
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:13.591
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:14.641
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:14.641
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:15.692
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:15.692
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:16.693
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:16.693
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:17.743
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:17.743
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:18.794
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:18.794
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:19.844
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:19.844
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:20.896
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:20.896
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:21.946
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:21.946
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:36.581
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:36.581
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:37.631
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:37.631
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:38.681
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:38.681
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:39.731
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:39.731
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:40.781
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:40.781
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:41.831
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:41.831
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:42.881
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:42.881
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:43.932
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:43.932
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:44.983
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:44.983
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:52.266
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:52.266
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:53.316
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:53.317
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:54.367
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:54.367
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:55.417
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:55.417
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:56.467
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:56.467
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:57.468
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:57.468
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:58.518
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:58.518
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:34:59.521
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:34:59.521
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:35:00.561
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:35:00.561
    !MESSAGE Problem occurred in auto-refresh native code: 5.
    !ENTRY org.eclipse.core.resources 4 1 2014-07-16 17:35:01.611
    !MESSAGE Problems occurred refreshing resources
    !SUBENTRY 1 org.eclipse.core.resources 4 1 2014-07-16 17:35:01.611
    !MESSAGE Problem occurred in auto-refresh native code: 5.
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    !MESSAGE Problems occurred refreshing resources
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    Thanks for the reply srvikram13, I really appreciate it.
    Unfortunately this did not solve my problem.  The application was developed in Flex sdk 4.1 and I have installed the 4.1 sdk and told the Flex Compiler to use that specific sdk to no avail (I even re-tried per your post, but no success).  The fact is that the project compiles fine with either 4.1 or 4.5 sdk, it just has issues finding the imorted classes until I manually open the class files.
    Further debugging and info:
    I actually thought I had it fixed for a second.  I renamed my "com" directory and right clicked on "src" and chose "New" > "Package" then repeated that for each directory under "com".  I then closed FB and in windows explorer copied my original com directories into the new one created by FB.  When I launched FB and opened the main file all my imports were recognized!  I then closed FB and re-opened again to see if it was truly fixed and ... epic fail.  The squiggly underlines are back and FB doesn't recognize any reference to them.
    I also found that even if I navigate to the class files in the Package Explorer then right click on the file and choose properties, then click cancel (never opening or changing anything) the reference to that specific file is now valid... at least until I close and reopen FB.
    Any other ideas?

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