www.makemkv.com

I've tried to find the fix here, but haven't been able to. What am I missing?

Actually that is what I'm doing if there is issues with Handbrake. If there is I go to MKV and let it do it's thing directly to the disk, otherwise you are correct in that you have to many variables.

When I use MKV on these, the subtitles automatically show up and I can't get rid of them. What am I doing wrong?

I seem to have the opposite problem.... I can get rid of the subtitles, esp in Iron Man 3 and Star Trek