I thought I would test it, it works for me. I have four one hour episodes queued up, and it is on the second episode. The computer is a Dual PowerMac G5 2.5, PCI-X, running 10.4.4.
You might try a Permission Repair.
Unfortunately, Versiontracker, et. al. don't mirror their files.
Stuff like this is why I save the installer file to a folder that contains downloaded software. This is especially important for the "grey" apps used to crack copy protection because those get taken down very often after a C&D letter. See if you can PM me, I can dig up my copy if you like.
I also do a system backup before doing any update that might alter the system, any update that requires a restart is a good rule of thumb, but I think backups need to be done more often than that.
This is a slimmed down version of Handbrake for iPod, it is still available:http://www.isquint.org/handbrakelite/