Check your network settings, port forwarding, firewalls, etc. Even if you don't plan on using it for your downloads, you might want to give Azureus a try, it has a testing utility that might help diagnose your problem, which is probably network related.
Could just be that one torrent. Maybe the tracker went down temporarily. Maybe they started blocking Transmission (some torrent trackers do). Maybe there are no seeds, and everyone is stuck at 97%. Give it another few days and then post a comment on the tracker site where you (ideally) downloaded the torrent.
Help... im downloading a few episodes of prison break... and all was well... then they all stopped downloading... so i paused them all thinking i can resume them and all will be good... so wen i paused it just froze... application not responding. and i cant resume them from the begining... what should i do to not lose my files?