encode in x264 mkv VFR mode from .ts ..!
 

the problem fixed

You have to trim before creating the tfm.txt in the first pass... I'd think.

Because of the trim not all frames are processed. But with tfm.txt before trim in first pass, it'll expect entries for all frames from source in the second pass. Which there aren't. Hence above...

Mediainfo is dumb, trust your timecodes. Mediainfo averages stuff, and it even does a bad job of that. Your timecodes will accurately show you how it is.

And ease off on the coloured/huge text :/

E~