I think performance of your HDD(USB 1.1?) could be an issue, Since i had the same problem when i was using older USB thump drive. Recenly i got new WD 1TB external harddisk(USB 2.0) and all the movies running fine, i mean no problem with FF.
I dont think even the HDD is a problem. Since the same issue is also there when I burn these avis on a DVD. I am unable to jump to a particular time in the movie. I am able to fast forward. That is not the issue, the issue is I cannot jump to a particular time.