lost preferences etc.

Used winxp repair function, booting from cd.
Before this I used the file and settings transfer function and saved settings to my hard drive.
After doing this everything looked normal. I loaded Mcaffe security suite and rebooted, every thing normal. I reloaded all the winxp updates and installed, all 64, everything went normal. Rebooted everything came up as normal. Didn't need to use file and transfer function to put things back. Everything was as before. I checked browser and email functions, all was ok.
I switched users to set an email account in the other user. Didn't have the info that I needed so shut down the email program. When logging off and going back to the orig user is when I lost all of my settings. I tried using file and transfer function but that was unavailable. My browser, email client, icons on desktop, picture for wallpaper etc. no longer has my preferences.
When booting one splash screen comes up saying:
invalid boot.ini record
booting from c:\windows
I have tried different system restorals, with no luck.
Any help?
thanks