I was trying to use h264 TS Cutter and that would give me an error of "It was not possible to write the Transportstream. Unable to read beyong the end of the stream." when trying to process the section i had selected to cut, so that lead me to TS packet editor and both didn't work. Last night i turned off "Enable Multi-Record support" and recorded an hour long show. This recording was fine in both TS packet editor and h264 TS cutter. If that has fixed it for me i am willing to live without mult-record support.
Edit: that didn't fix the issue. My recordings still can't be edited in TS packet editor or h264 TS cutter.
Edit edit: OK found the problem was actually in TS packet editor, I changed the timestamp from PTS to PCR. I havn't found an option like this in h264 cutter so I won't bother using that.