mkvmerge producing something really weird looking

[Mr Alpha]

I've been ripping a DVD (Sniper), with DGdecode/avisynth/subrip/x264/mkvmerge gui. The encoded video coming out of x264 looks perfectly fine, but when I use mkvmerge to mux in the audio, subtitles and chapters the video starts looking really weird. Like this. (http://mralpha.s3.amazonaws.com/Sniper.mkv_snapshot.jpg)

Is it a bug of some sort in mkvmerge, or am I doing something wrong?

[Atak_Snajpera]

disable dxva and use other player

[Mr Alpha]

disable dxva and use other player
I'm not using any form of DXVA. ffdshow is doing the decoding.

Opening the file in VLC the video looks correct but it seems to think the movie is three hours long (in reality it is only 1h 30min). If I seek to the second half it is only black and VLC crashes.

EDIT: OK, so after some combinatorial muxing it seems the subtitles are the problem. If I leave them out it works fine. So it could be either SubRip creating weird subtitles, or VSFilter which is the real problem.