Thanks for you reply. This got me thinking. Are you able to setup up a raid 0 system to test on?
I have 2x 150GB raptors in raid 0. Perhaps CCleaner does not like raid 0.
This is a rather large issue if this is the case, because raid is being more and more mainstream for gamers.
This is definitely not a hardware issue, I never receive any CHKDSK errors, even after having windows installed for weeks. It only happens after I run CCleaner's "Cleaner".
All 3 of my hard drives are in healthy condition. I've used windows for a few weeks without running CCleaner - there were never any CHKDSK errors. As soon as I run CCleaner and restart, I get chkdsk errors. This basically proves its software related - Or that CCleaner does not like my hard drive setup which is 2x Drives in Raid 0, and 1x Storage drive outside of the raid.
Also i'd like to say that this is not caused by cleaning registry. It is caused by running the temp file cleaner via CCleaner. I've figured this out on yet another test I did. I have all boxes checked on the cleaner.
The following programs are programs that are detected with CCleaner that I have installed on my computer:
Firefox
Foxit
Sun Java
Media Player Classic
Windows Media Player
Winrar
Windows Defender
MS Paint
MS Word
RegEdit
I'm pretty sure if you setup a computer in Vista 64bit (ultimate) using 2 or more drives in a raid 0 array, install the programs I have listed, check all boxes in the CCleaner, run it, and restart you will get CHKDSK errors. However these errors are not reported if you boot to CHKDSK. You must go to run > cmd > chkdsk.