Disk Problems, OSX partition will not repair is Windows CHKDSK the culprit?

Hi,
I have both Snow Leopard (fully updated) and Windows 7 on Bootcamp partition on my MacBook Pro.
Repairing Permissions on my Mac OS 10.6.4 partition had become a very regular with 'Java' permission problems always seeming to be a very regular and common one.
Anyhow, I thought it appropriate and logical to run the WIndows 7 equivalent of disk-verify/disk-repair/permission-repair and therefore run CHKDSK at 'CMD' level and this appeared to run accordingly without problems.
At some point/days later, my Mac OS appeared to be slow and having a lot of spinny-ball, therefore verified Macintosh HD volume-disk with Disk Utility and showed to have lots of problem. Disk Utility Repair has failed having tried it many times and not even Drive Genius 3 is able to repair or rebuild it on this occasion however I was able to run a 'Scan' on it from Drive Genius 3 and it reported thankfully that there was NO bad blocks.
The error thats returned repeatedly when doing a repair is "Incorrect number of thread records" which is reported immediately after "Checking Catalog File"
Not keen on the thought of having to format, re-install and then re-setup the system even from a Super-Duper backup copy that I had made previously (minus some data since).
However, my questions are:
1. Is it possible that the Windows 7 'CHKDSK' command may have possibly caused this despite the fact that it would have or should have only performed it's operations on the BOOTCAMP disk partition?
2. Is it possible to reformat and restore any previously backed-up images to a single disk partition _without upsetting the other Partition and OS_ residing on it (albeit on the same overall physical disk), i.e. Restoring my Mac OS X SuperDuper backup image back onto the current Mac partition... and would the same apply if ever having to restore a Windows 7 Acronis backup image back onto the current BOOTCAMP partition.
3. Would there be another alternative before a drastic reformat and recovery of the Mac OSX partition (if that's even possible without affecting BOOTCAMP - from question 2 above)
Advice would be much appreciated, many thanx.

At the time I had run the 'CHKDSK' command from within Windows, from the 'Run' command prompt located within the Start Menu.
Fortunately I still have the previous HDD that originally came with the MacBook Pro before I upgraded the internal drive some time ago and therefore I have been able to boot externally from this and continue to do so until I've decided what to do, which looks like a recovery from the previous super-duper backup will be inevitable.
I guess I'm unlikely to come across any software or fix that will be capable of correcting the 'faulty number of thread records' being reported after the 'Checking Catalog File' disk repair check routine, however if I find a solution then I'll post it here, otherwise an eventual recovery/install it is.
Under Fortuny's revelation, I will procede with MacDrive with caution and probably disable it if ever running a Windows CHKDSK again (if indeed this is the underlying cause of the problem). And under your advise 'The hatter' I shall certainly look into the Windows system file checker alternative, thanks.

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****Click the White thumb to say thanks****
****Please mark Accept As Solution if it solves your problem****
****I don't work for HP****
Microsoft MVP - Windows Experience

Disk Problems, OSX partition will not repair is Windows CHKDSK the culprit?

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