HD video / MKV unexpected end/cutoff

I have a problem which appeared first, at least in my case in v0.6.1 (right now I am running 1.0pro). The issue is that some of my HD videos end unexpectedly, usually at around the 60 minutes mark. When I downgrade to 0.6, this bug goes away (eg. my Samsung C TV plays them properly until the end). Any advice on this?

[zip]

Try the newest FFmpeg. Otherwise check the log for any errors.