Well, I just experienced audio skipping last night using tsmuxer.
The original movie is DL and shrink with BD Rebuilder resulting 19GB video and 500MB DD AC3 audio. When I saw the video size I thought I can fit the original Dolby TrueHD. Extract Dolby TrueHD using tsremux (3.4GB) and it did fit BD-RE 25GB. However the audio skipped, video is fine.
So I use tsremux again but this time using AC3 audio (downcovert from Dolby TrueHD), burn to BD-RE both video and audio are fine.
Since I still have the m2ts of video + Dolby TrueHD from previous tsremux, I re-ran the m2ts with tsMUXer and now both video and hidef audio are fine.
I think somehow tsremux doesn't like some hidef sound (Dolby TrueHD in my case).