jmone,
Perhaps you could clarify how you are viewing Captain Phillips in MC. Are you using AnyDVD as a plug-in for MC?
The method I have seen cause problems is to use MakeMKV to backup the Blu-Ray disc (not to create an MKV file) and MC recognizes the BDMV folders and plays the movie, just without the forced subtitles. I've also seen the same issue on Elysium. And no settings I played around with allowed only the forced subtitles to show up. The common thing about the forced subtitles in Captain Phillips and Elysium is that they are a flagged subset of a full subtitle track. Other titles that have the forced subtitles as a separate track work just fine once you choose the appropriate track.
So assuming you're using AnyDVD to play the Blu-Ray disc, I'm wondering what could possibly be different about the backup produced by MakeMKV vs. AnyDVD?