Adobe Premiere CS3 not accepting video files and out of synch

Hi everyone,
Just a quick summary of the project I'm working on:
Approx 26 hours of HD footage captured from Canon XH-A1. My system specs are:
- Intel Quad Core Q6600 2.4Ghz CPU
- 2Gb RAM
- 4 X 500gb SATA 2 Drives
- At least 60 GIGS of head room on each drive
- Windows XP
Anyways, onto the PROBLEM:
I downloaded the CS3 UPDATES the other day to find that all my video files had to be re-indexed and after this had been done my TIMELINES had all been adjusted and altered (sometimes only a second or two off, sometimes more), so basically my entire project was out of whack. I googled this and found that I was not the only person experiencing the problem.
Since my project has taken me 9 months so far to complete this is a huge deal.
I saved my project plus I had a backup copy from before I did the updates, and I then uninstalled CS3 and then re-installed it WITHOUT the latest updates.
I thought this would fix the problem but I was WRONG!!!
I loaded up the project and it asked me to locate the video files - I directed the program to them and then this error message popped up:
"The selected file cannot be linked because its type (video) does not match the original file's type (audio and video)"
I pressed Cancel and entered the project, where all my video files were now OFFLINE.
I then found that by linking a video file 1 at a time (or as most as 6 at once) the error message would not pop up (???) and it could link up to the video files.
BUT the problems continued because I found that most if not all of the video files were now OUT OF SYNC and hence unusable. The original files of course are NOT out of sync so this is a program error.
I have done various trouble shooting strategies to locate the cause of the error to no avail.
If anyone can help me it would be greatly appreciated, my project os of immense importance to me.
Regards,
Jeremy.

Ok, I installed the first update so I have version 3.1 which WAS working fine, but when I tried to load up the project and link the video files this message keeps popping up:
[..\..\Src\Win\WinPathUtils.ccp-553]
Also, no, my project is not 24P, it is 25P 50i.

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