2 different issues while converting

[rs232]

1)
There are some movies I've downloaded where Media Player Classic is not "easy" skipping to a certain point.
If these were old avi file I would have thought of a broken index but they are all MP4 or MKV, I've tried to repair with Meteorite the MKV but same issue.
The funny thing is: If I convert them with e.g. Handbrake even the destination file experiences the same problem.

2)
A slightly different issue I'm experiencing is where a source file is large in size but good quality; so when I convert it into a smaller .MKV the result is a terrible video quality file with blocks of pixels appearing randomly.

This happens with certain files only and not very often, I'm wondering if there's anything I could try to do differently

Thanks

[LigH.de]

1) Just like AVI, also MP4 and MKV have keyframe index chunks, which may be missing or corrupted if you download movies (either transfer issues, or originally created by stupid people). The recommended original multiplexing software for such containers (e.g. MP4Box and MKVToolnix) may repair missing indexes, or at least display sensible messages if it can't.

2) MKV is a container format. If you reduce the size during conversion, then you converted the video stream into a new video format, and that way you will certainly loose some amount of quality, especially when you use even less bitrate than your original. On top, if you had some data corruption in your downloaded video, a converter will expose them as video corrpution, even though you may not see it just as obviously in a media player.