Help - odd file system corruption.

Question

I have something very worrying going on on my system. The contents of an important folder is being listed differently in 3rd party applications vs the Finder. Apps which use a non-OS file browser cannot see the up to date contents (its an important project I'm currently working on), instead they only list folders from months ago which are now long gone and don't show the current true contents at all. Eg Cinema 4D's Content Browser can't see the current files correctly, but it can just fine via the OS Open/Save dialog.
Even worse is that Chrono Sync has exactly the same problem. When it syncs it correctly lists some of the current files that I'm working on, but in the Anylise section, manually drilling down to my working project folder again shows the incorrect contents!
I have copied the directories to a new HD but even THEY show the same errors when not viewing the contents directly with Lion file browsers***
I can remember once when I first saw this in Cinema 4D I immediately checked in the Finder - and the Finder showed the wrong contents too !- I refreshed the Finder window by clicking a different folder and back to the working directory which then updated before my eyes to the correct contents.
How can I fix this? It seems like there is an immenent serious corruption about to happen to my files and/or disk. Disk Utility shows no errors, nothing to repair. Can/should I use Diskwarrior or some other repair app. Help!
(***I just remembered that I used CCC in block level copy mode so this might account for why the corruption has been transferred to the new drive. I am copying the working directory to the new disk using drag nd drop in the Finder to see if that helps. However I still need the underlying corruption in my User folder repaired)

Answer 1

Yes, I have quite a comprehensive backup strategy in place (involving a Drobo for nightly CCC backups, a CCC nightly bootable disk clone and TM for hourly backups). The Block Copy is for the bootable disk. The nightly Drobo backups are done with vanila CCC file copying,
Disk Util does not find any problems, neither did Disk Warrior. SMART is all OK.
However as I said, the problem is present on one of the backups as well which has put the integrity of the rest of my backups in doubt. also I have tried a direct Finder copy to a new drive (instead of CCC block copy) but the problem persisted.
I have however come up with a temporary fix: I moved the current folder to the trash, navigated to the parent directory using Cinema 4D's Content Browser wherein it 'saw' the ancient folder once again. This errant folder was now also visible in the Finder since the original folder (which has the same name) was now in the trash. I renamed it and moved it to the trash too. Then put the original folder from the trash back into its parent directory and emptied the trash removing the errent folder for good. It seems that did the trick of updating whatever caches or databases were broken and all my apps can correctly see the correct folder and its contents again.
This 'historical' version of the folder was being linked to by 3rd party file browsers I think because in the past it had the same name in the same location as the current folder. Where and how the OS got confused is still a mystery. Does it keep different file system records for the finder vs other apps?
I am not 100% convinced this is a true solution though as there may well be a deeper problem afoot.
I would like to see some kind of error/fixed message from Disk Util just so I know the OS is on top of this problem. As it stands my Mac thinks everythin is A-OK.