The problem with converting mkv to mp4 is that the HDR-FOX only seems to play mp4 files with AAC audio. If you convert say an mkv with H264 video and AC3 audio to mp4 you have to transcode the audio too. You can do this on the HDR-FOX itself with ffmpeg as long as it is only audio transcoding that is required.
1GB mkv file on i3 PC using AviDemux:
Time to convert from mkv to mp4 and save: <30secs
Time to convert inc. recoding audio from AC3 to AAC: approx 1 minute.
Correction: In my previous post I mentioned MkvToolnix. I should have said AviDemux - MkvToolnix has mkv output only.