Given GBPVR is no longer being updated, I'd try it with NPVR. If you have the same problem with NPVR, then I'll add some logging to find the cause, and I'll fix the problem for you.
Thanks sub. I have done a trial with NPVR and so far the playback is ok with the mandatory TS Mux. I'll keep testing with new NPVR versions as they are released.