@glisoni
You do not get any option windows, don't you? One possible cause could be the UTF format of the embedded subs: only UTF-8 is accepted so far. Could you copy&paste here the mediainfo of your mkv (subs section)?
@Adub
yes, you are right, it is quite odd... QuEnc is a ffmpeg spinoff... It could be Wavi having problem with DTS-HD tracks.
Bye