www.makemkv.com

So, I've just started using this app & there are a few weird errors when playing back the first episode of each disc I rip for the Shout! Factory release of Kyoryu Sentai Zyuranger. When I go to play these particular episodes in VLC, none of the visuals play & the subtitles don't come up either until I pause the playback (for the subs, I mean). In Windows Media Player, the visuals & audio play fine, but the subs don't come up as they should. Instead, they only come up in sporadic intervals & are colored blue rather than yellow like they should be. Is there any way to fix this?
And, yes, I've tried copying the episodes again. No dice.

.mkv files have various flags that can be set for the different tracks contained in them. The utility MediaInfo can show you lots of details about your .mkv files. Notably, it can show you if the 'default' flag is set to true for the subtitle track.

It is possible to control the setting of the default flag and the forced flag (for forced subtitles) in MakeMKV when you rip. It is also simple to change it later with the MKVToolNix tools.

I have limited experience with VLC and almost zero experience with Windows Media Player, but I would expect most players to behave properly if a subtitle track is defaulted to true.