hehe, whoops, looks like I forgot one step. I extracted the .sup files with MKVExtract, *then* I opened the .sup files in BDSup2Sub and converted them to .sub files, and it also created a .idx file for each stream. The newest MKVMerge will accept these .sub (actually the .idx) files and mux them right into the MKV for me.
Sorry, that's a big step. It doesn't take any time though. I used it to pull out forced subs only from Defiance, which worked fine, but is the only disc I have with the forced subs, so I couldn't test on anything else.
so a recap, MKVExtract to get the sup files, BDSuptoSub to convert them, MKVMerge to add them into the file, you must move them up in the order to get them before the sup files and they will all show up in my player; the sup files won't play, but everything else works fine.
Sorry for the confusion