Upgrading/re-installing application quits for User

When I re-instllaed Sorenson Squeeze it would not start "The application unexpectedly quit... etc" No amount of re-installing, optimizing, etc would fix this. The work-around was to create a new User and install it from there. No more problems.
Then the same thing happened with an upgrade of Motion. "The application unexpectedly quit... etc". Installing it from the apternative User solved the problem, but Motion will only run from that User account.
Today it happened to a colleague who was upgrading iShell from 4.0r9 to r10. He kept receiving a "Process Error (-600)" and nothing would open. I suggested the new User trick and it worked for him.
A nice work-around, but there is obviously a problem here. This did not happen in 10.3. Any ideas about what's going on?

Thanks macjack for a speedy and really helpful reply - it's filed. I've already tried the fonts and permissions, but I just went through your suggestions again with Motion. No joy I'm afraid. Here's the relevant bit of the crash report (I think - it's witchcraft to me)
Thread 0 Crashed:
0 com.apple.CoreFoundation 0x907c7af0 CFGetAllocator + 24
1 com.apple.CoreFoundation 0x907c84ac CFURLCopyFileSystemPath + 28
2 Ozone 0x011b6df4 +[OZFileSystemLibEntry buildTree] + 532
3 Ozone 0x01356fb0 -[OZFileBrowserController buildTree] + 96
4 Ozone 0x0135b920 -[OZLibraryControllerBase viewDidLoad] + 3888
5 Ozone 0x013569b8 -[OZFileBrowserController viewDidLoad] + 104
6 Ozone 0x0108d8a0 -[OZPBXModule _viewDidLoad] + 288
7 Ozone 0x0108d2ec -[OZPBXModule view] + 124
8 Ozone 0x0117a5f4 -[OZTabbedModule addTabViewItem:module:] + 68
9 Ozone 0x01146710 -[OZLibraryInspectorController viewDidLoad] + 128
10 Ozone 0x0108d8a0 -[OZPBXModule _viewDidLoad] + 288
11 Ozone 0x0108d2ec -[OZPBXModule view] + 124
12 Ozone 0x0108fda4 -[OZPBXWindowController _installModuleView] + 100
13 Ozone 0x010905c4 -[OZPBXWindowController initWithModule:] + 68
14 Ozone 0x0108f760 -[OZPBXModule setWantsModuleWindow:] + 192
15 Ozone 0x011464c0 +[OZLibraryInspectorController instance] + 96
16 Ozone 0x0114946c -[OZScreenLayoutManager loadInitialLayout] + 92
17 Ozone 0x0114964c -[OZScreenLayoutManager loadInitialDocLayout:] + 60
18 Ozone 0x0114e304 -[OZDocWindowController windowDidLoad] + 852
19 com.apple.AppKit 0x937f2ca4 -[NSWindowController _windowDidLoad] + 332
20 com.apple.AppKit 0x937ef678 -[NSWindowController window] + 128
21 Ozone 0x01083260 -[OZObjCDocument showWindows] + 192
22 com.apple.AppKit 0x9383bed4 -[NSDocumentController(NSDeprecated) openUntitledDocumentOfType:display:] + 132
23 Ozone 0x013a9228 -[OZDocumentController openUntitledDocumentOfType:display:] + 232
24 com.apple.AppKit 0x9379fff0 -[NSApplication sendAction:to:from:] + 108
25 com.apple.prokit 0x962c5bdc NSProCenterRect + 32000
26 com.apple.AppKit 0x9379ff24 -[NSControl sendAction:to:] + 96
27 com.apple.AppKit 0x9379fe04 -[NSCell _sendActionFrom:] + 156
28 com.apple.AppKit 0x937b9e1c -[NSCell trackMouse:inRect:ofView:untilMouseUp:] + 1020
29 com.apple.AppKit 0x937b9a04 -[NSButtonCell trackMouse:inRect:ofView:untilMouseUp:] + 564
30 com.apple.prokit 0x962f6850 NSProApplicationLoad + 197300
31 com.apple.AppKit 0x937b9428 -[NSControl mouseDown:] + 536
32 com.apple.AppKit 0x9375ac30 -[NSWindow sendEvent:] + 4616
33 com.apple.prokit 0x962e3858 NSProApplicationLoad + 119484
34 com.apple.AppKit 0x93703c74 -[NSApplication sendEvent:] + 4172
35 com.apple.motion 0x00010a58 0x1000 + 64088
36 com.apple.AppKit 0x936fb0b0 -[NSApplication run] + 508
37 com.apple.prokit 0x962c6514 NSProApplicationMain + 288
38 com.apple.motion 0x0000ec24 0x1000 + 56356
39 com.apple.motion 0x0000d7e8 0x1000 + 51176
40 dyld 0x8fe01048 dyldstart + 60
Dual 2.3 PPC G5   Mac OS X (10.4.6)  

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