I've noticed when playing many original Blu-rays that they appear to have no subtitles enabled, while still showing forced subs. Movies ripped with ClownBD don't work this way.
So I did a little research and figured it out. Updated my wiki page on Forced Subs with ClownBD
to explain it, under the "Advanced" section. It requires a lot of manual steps, but results in a nicer final presentation.
Today I ripped Twilight: Breaking Dawn Part 2, which has two forced subs starting at 0:52:59 that BDSup2Sub doesn't quite understand. The forced subs that it extracts are not quite right (first one is way too brief). Rip it using my "Advanced" method, and everything turns out great.