Bleh, well I see the problem was still not addressed in build 829. Actually while writing this post I was making a Matroska sample file in case you needed one to verify the problem. I found that I made a large mistake the other day, it is the presence of a VobSub track not SRT (which totally explains why an OGM with an SRT has no problems, and also why the problem wasn't fixed already....it wasn't SRTs at all). So just replace SRT with VobSub :)
This sample I provide here is very simple. BlankClip video + an essentially blank vobsub, there is only 1 picsub. Nothing else in the file at all really, which will cause the "crash". The simple presence of the vobsub track, whether it is the default track or not, is what seems to cause it. The options I turned on/off are the same as the post above, used with Haali's Media Splitter and VSFilter. The only change because of my mistake is that VobSub options are also disabled.
Edit: Forgot to add link.
http://rapidshare.de/files/13580081/..._test.mkv.html