Update: I'll leave the previous suggestions I wrote first below, but I may have found a simpler solution for MPC-HC users.  There's an update to part of the Windows video system responsible for subtitle rendering and some fansub sites are already using tools based on it.  There's information and a link from the UTW homepage to it at http://utw.me/   It may fix this and other subtitle problems some people have been having with gg, utw, rori, etc.  No promises about fixing this specific one, but maybe.  Note: During installation it provides specific instructions for MPC-HC users.


My previous comments, in case they're still useful are below.  I haven't used the UTW upgrade on the machine the note below was written on:
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Actually, this ep2v2 plays subs fine in my MPC-HC even though under Navigate/Subtitle Language it is listed as "S: (Undetermined) [Unknown 0]".  So it can be done.  I hope that's good news.

It probably works for me either because I'm also using the Haali Media Splitter, and/or because I set an Arial default font in the MPC Options/Subtitle menu and/or because DirectVoxSubs are automatically invoked when needed in my configuration.  Also, I checked the box "Position subtitles relative to the video frame" to be sure the subs don't disappear above or below the screen.

If you want to try any of this:

1. Under View/Options/Subtitles be sure you have a system font selected as DEFAULT (1) and check the box for "Position subtitles relative to the video frame"
(Also, under Video rendering: if you're not using Overlay, then several other settings have to conform to the rendering system you use in order to have subtitles displayed properly.  And there are other settings elsewhere that can also affect subtitles, but if subs are generally working for you I assume they're ok as they are.)

If that's not the problem, then:
2. Either get the CCCP package which includes MPC-HC and Haali, or get and install Haali separately.

When installed and configured correctly, your system tray will contain 4 extra icons when using MPC-HC: FF-Audio, FF-Video, DirectVoxSub, and Haali.
(I believe DirectVoxSubs is invoked by an FF-Video menu, but it's a long time since I did this.  I don't like MPC-HC.)

These subs also worked with potplayer and kmp, both also configured with Haali.

http://cccp-project.net/

http://haali.su/mkv/  Download the MatroskaSplitter installer and install it on your system.  Then select it as the media splitter in MPC-HC Options.

(Haali is needed to play Coalgirls and other groups that use Ordered Chapters with separate OPs and ENs.)

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Lastly, I should say the fact that it doesn't work for you means the fansub group should release another fixed version.  This is a new group, and their first project, and...well, I wouldn't want to discourage the only group subbing a show I'd like to see...

Until then, if any of the above suggestions work on this version, you'll have a more bullet-proof video player.
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Update: There have now been thousands of downloads of ep2v2 and I haven't found even one other complaint about missing subtitles.  So I don't think there's anything the fansub has to fix with this release.  You could try an uninstall and reinstall of your video software, if you want to.

Since all the video players are free, I keep several on my home machine up to date.  That's another easy way to be compatible.  For example, gg's version of the 8th Grader Syndrome show has some subs that don't show up on KMP or Potplayer unless you disable gg's default font.  But it plays without modification on MPC-HC/64, so I just use that for their shows.

Works as long as you use players and settings that don't alter the entire system messing each other up.

But regardless of player, the two things I mentioned may not be optional:  
1. The Windows Directshow update at UTW.  They warn that subs may flash or disappear from this point forward without this update.  If they ever do for you, this might be the only solution.  If subs haven't, fine until then.
2. Haali.  Some anime fansub groups slice off the opening and closing sections and have them separate to save a little on file size.  As long as you can avoid these groups, fine.  Otherwise, I don't think any video player reassembles these parts without Haali, even now.

I should mention, some of the best versions of the best shows ever in anime (best translations, best editing, best video) are only available in Ordered Chapters format.