I decided to back up my glee dvd discs and found that after running the videos through handbrake and choosing the vobsubs as the main subtitles that after the mkv are authored and burned to blu-ray that some of the subs didn't show up.

After a lot of muxing and testing i found that if the sup starts with no dialog(empty) in line one that the subtitles will not show up.What i did is ran the sup through BDSup2Sub and excluded the first frame of the subs with no dialog and saved then the subs would show up.

With multiAVCHD 4.1 if you are adding the videos with the new sup then you have to add as an external sub or it will no show up if its muxed into a mkv.