Yeah, if you're running an updated version of OS X compared with what's on the install disc and you repair from the install disc, you can run into problems. Have you tried going into Single User Mode? Hold down Command-S after the Mac startup chime and once you see the Unix text go across the screen, let go of the keys.
At the command prompt you'll see some instructions on what to do to run a repair on the disk. Something like "/sbin/fsck -yf" is what you'll have to type. hit return and have it go through it's sequence. If you get a message that says "FILE SYSTEM WAS MODIFIED," that means it fixed something. Run the command again until you see a message saying that the Macintosh disk is OK. Once you get that message, type reboot and see if it boots back in.