Funny thing is, I know that one of the devs, at least a while ago, always worked through remote desktop and all that did definitely work through RDP back then.
Doesn't matter - they'll fix it.
This thing is complex as hell (which is hard to tell by just looking at the GUI) and they decided not to leave all tasks to ffmpeg etc., like most other tools do. This means, CloneBD has to fight with all those little quirks in AVC, BD, TS, different players with different interpretations of specifications, .... that the ffmpeg crew has been fixing over the past years.
That decision was made long ago, as ffmpeg/libav simply didn't do the job right, but meanwhile I guess that's no longer valid.
But now there's no point in moving over to "full ffmpeg mode", better to get everything fixed and then have full control over the software and not be dependent on some 3rd party tool too much.
Just a little explanation for why it's taking so long to get everything to work for everybody. Just far too many use cases and varying source material.