To be honest, I dont know. I'm no longer making changes to GBPVR, so I cant add additional logging etc to track down the cause. You may need to stick with TS Mux if that's working.
NPVR (the GBPVR replacement) always produces .ts files, so unfortunately doesnt help you too much with this problem.
Thanks for all your help, I think that I'm going to give up on this one. Using the .ts format isn't so bad, my main issue has been audio issues with audio described programs. When I convert them to AVI using mencoder, I sometimes get the audio description rather than the main audi track. Never been able to figure this one out and it wasn't a problem with .mpg.