The issue redrapis620 is talking about is that the HUB, and SMP for that matter, can't read the "libmkv 0.6.5" writing library that is used by the current version of Handbrake. On the HUB the issue started with the first 3.**.** FW (it may have been present in 2.08.13) and is still present in the latest (3.04.17).
This is not an issue with HUB FW 2.07 and the same mkv's play fine, so it was something introduced in the FW.
I'm not sure if this is the same issue that the other memebers have with their external drive mkv's, but if they encoded the mkv's on the internal drive with Handbrake 0.9.5 and the mkv's on the external drive with Handbrake 0.9.6 then this would be why the internal mkv's play and the external don't. This is because HB 0.9.5 uses the "libmkv 0.6.4" writing library which the current firmware will read.
Anyone wanting to see if this is there problem should download Mediainfo then open the file that will not play or freezes with Mediainfo and look to see if the Writing library says: libmkv 0.6.5. If it does, then this is most likely why you are having issues with that file.