I have this same problem with MKV, though I can't get OGM files to work at all. ConvertX runs about 3 seconds after I press CONVERt and then stops saying it converted successfully. That's for the OGM files.
For MKV I wasn't having trouble for a while, but I recently tried to convert some MKV with Dual Audio MP3, and the sound is out of sync with the video. I add subtitles manually, which match the sound, but of course not the video. On top of that, I've been converting MKVs for a while with no problem -- 4 200mb files usually take an hour and 15 minutes. NOW, it starts at 20 hours, goes up to 30, then to 45 hours!!! Yeesh.
I can't see that these MKV are different than others I've tried. They don't have h.264, which some people say complicates things.
Any help greatly appreciated (that, or give me a good program to convert MKV to AVI. I use AlltoAVI, but I get a sound sync problem there too! RiverPast isn't any better. Same thing. Plus, RiverPast only uses the first audio segment, which isn't the one I want.)
Besides this minor bitching, ConvertX is still the best out there. Hope there's any update soon to resolve the MKV thingy. I was delighted when it added that format. OGM, though. What's up with that?