I found the reason for the wrong encoding of my videos.
ffms2.dll with version 2019-08-30 StvG is producing faulty videos for me. If I use the "old" 2.23.1 (latest version) from
the website, then my video is encoded just fine.
I noticed, that during the x264 encode, the amount of frames was considerably higher than with the ffms2.dll shipped from StaxRip 2.
I uploaded
an example. No additional filters needed.
Old ffms2.dll shows this info in StaxRip:
New ffms2.dll shows this info in StaxRip:
Notice the FPS of the Source Video.