Xcode snapshots problems

It seems in Xcode I'm at a point where the snapshots will no longer work for me. When I make a new snapshot, it always shows every file in the project in the "Files Added" category and there will not ever be files in the "Files Changed" category. Older snapshots a few files in the "Files Changed" category but no new ones do.
Does anyone know what to do here?
I've tried removing directories in ArchiveDirectories, editing the Snapshots plist file, removing the snapshots image (~Library/Application Support/Developer/Shared/SnapshotRepository.sparseimage), among other things.

That was easy. The DU output appears in the console log. Here it is:
12/23/08 12:30:27 AM Disk Utility[9894] Repairing permissions for “Hina”
12/23/08 12:30:27 AM Disk Utility[9894] Reading permissions database.
12/23/08 12:30:27 AM Disk Utility[9894] Reading the permissions database can take several minutes.
12/23/08 12:36:13 AM Disk Utility[9894] Permissions differ on "private/var/log/secure.log", should be -rw------- , they are -rw-r----- .
12/23/08 12:37:03 AM Disk Utility[9894] Permissions differ on "System/Library/LaunchDaemons/com.apple.usbmuxd.plist", should be -rw-r--r-- , they are -rwxr-xr-x .
12/23/08 12:37:04 AM Disk Utility[9894] Warning: SUID file "System/Library/Filesystems/AppleShare/afpLoad" has been modified and will not be repaired.
12/23/08 12:37:04 AM Disk Utility[9894] Warning: SUID file "usr/bin/setregion" has been modified and will not be repaired.
12/23/08 12:37:12 AM Disk Utility[9894] Warning: SUID file "System/Library/PrivateFrameworks/Install.framework/Versions/A/Resources/runner " has been modified and will not be repaired.
12/23/08 12:37:12 AM Disk Utility[9894] Warning: SUID file "System/Library/Printers/IOMs/LPRIOM.plugin/Contents/MacOS/LPRIOMHelper" has been modified and will not be repaired.
12/23/08 12:37:12 AM Disk Utility[9894] Group differs on "private/etc/cups", should be 0, group is 26.
12/23/08 12:37:12 AM Disk Utility[9894] Permissions differ on "private/var/spool/cups/cache/rss", should be drwxr-xr-x , they are drwxrwxr-x .
12/23/08 12:37:22 AM Disk Utility[9894]
12/23/08 12:37:22 AM Disk Utility[9894] Permissions repair complete
Doesn't look like it should have helped Xcode at all. This is what I remember with certainty:
1. I made a snapshot days after installing the 10.5.6 update (directly from Software Update.)
2. I got the "(no changes)" message when comparing that snapshot with the previous one.
3. I quit Xcode, relaunched, and the problem had disappeared. All diffs showed up.
4. Days later, I made another snapshot and "(no changes)" appeared when comparing any snapshots. This time, quitting and relaunching Xcode didn't help at all. The 12-15 and 12-20 folders contained identical files despite my having made many changes.
5. I tried restoring the SnapshotRepository.sparseimage via Time Machine, mounting the image and looking for missing files, etc. Couldn't find any signs of corruption. Never touched any preferences files though. Nothing helped. This is when I made my original post.
6. Ran DU "repair permissions" just for grins, and suddenly "it just worked." The latest snapshot that I had made (the one that that seemed to trigger the problem) and all others now show the expected diffs, some of which are quite extensive changes.
7. Subsequent snapshots also show the correct diffs. So I thought DU had fixed the problem. Maybe not.
Now, here are some things that I did that directly affected the repository image. I just can't remember exactly when I did them:
- At some point I deleted a snapshot using the Xcode interface by choosing a snapshot and clicking Delete. I can't remember exactly, but I'm pretty sure I deleted the last one at the time (dated 12-20, which, when I mounted the image, contained files that were physically identical to the 12-15 snapshot's.) This would have probably happened at some point between steps 5 and 6 above, but I'm not sure.
- I'm pretty sure I made at least one other snapshot on the 20th, got the same "no changes" message, and just gave up fiddling around. Waited a few days, made a few more changes, then posted here.
Sorry for burning up all that bandwidth. It really doesn't look like permissions could have caused the original problem (the 12-15 and 12-20 snapshots containing identical files despite my changes in Xcode.) But somehow things are fine now.

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