Interesting. I happened to open my copy of DVDFab and found that was what you were using to set the Profile.
However, setting it to MKV did not impact UniFab at all. It still opened the first imported file (an MKV file) but set the output to MP4. In addition, my settings in DVDFab were set to MKV (except for the Mobile, so I set it to MKV, too).