Try an evaluation copy of VideoReDo.
Bring up their editor, but instead of loading your PS into it , from the pull-down menu, select QuickStream Fix.
Have it process your file, and write to disc.
Now, try
that program stream and see how it works.
I use
VideoReDo to edit out commercials, but it has a powerful feature to fix-up timing issues and other modest stream errors.
It may solve the problem you mention.
You'll have to request a trial key.
It's a simple operation, also on the pull-down menu, and automated.
That unlocks the program to run for a couple of weeks, without any restrictions.
If you don't, then it'll only output something like 15 minutes worth of video.