I've got a edit that i was working on in FCp 5.1.2 and reinstalled my OS and then FCP 6...now the edit looks correct by the thumbnails, but the wrong clips show up....re connect media doesn't fix it. it seems that the original master clip outside of FCP correspnds to all my subclips(example..if subclip reads 00:02:30:27, the master clip in QT corresponds to same spot)...but when I open same clip in FCP 6...the audio is out of sync and the wrong section of the clip shows up(example if suclips reads 00:02:30:27, it shows up at wrong section in viewer and timeline).

Try deleting your render files, all of them and re-render your project.
I found that any issues I have, a simple render deletion will fix it up.