Invalid security ID on files in a Vista – XP Dual boot system

I had a registry issue and wasnt able to get into the XP drive at all, so i booted from vista and did a chkdsk, and it took about 2 hours, and went through and reset all the security ID’s on my vista drive, i have reinstalled (repair re-install)XP about 3 times now and half the files in windows just simply wont read…….i cant install any updates (including SP2)and half the files are simply unreadable……. do you have any ideas to fix this that desnt involve deleting the whole drive? (as my uni work is on there) is there anyway you know to reset the security ID to something XP can read? i have tried chkdsk’ing in XP and have tried a million other things and nothing seems to work!!

Any help would be GREATLY appreciated.

Cheers