I have issues with several bluray ISO. Boxee is very picky about some bluray discs, in the end I had to rip just the movie and leave out all the extras.
Issues I had would be :-
1) Move would play for a few minuets, then repeat its self.
2) Movie would play one version for a few mins then play the alterative version
3) Movie would stutter really bad.
4) No bluray will play using its menu system.
5) Ripping Just the movie with the sound track you need should work, full bluray rips have always given me problems.
OP might not be able to run anydvd, and I have problems with some BD which were done with Anydvd. It seems to be the extras and the menus that are the problem.
Boxee is a good product - stop bashing it.
If we all include our setup we could all help each other better
My Equipment :- Boxee Box, Cat5e, Prosafe Gigabit Switch(s), Airport Extreme, WD ShareSpace, WD MybookWorlds, Qnap-TS412, Samsung PD59D550 3D TV, Panasonic BT270 (for optical audio)