Every mkv 720p file that I have put through mkvtools, has worked perfectly. I even add a 2ch track so the files are compatible with my atv2, ipad and iphone.
One movie (toy story 3) popped up a box saying it has something on it that might not make it work and to go to another screen and turn off something. Once I did that it reencoded the file. I then put the file back into mkvtools and pass it thru and it worked. So I'm guessing files that don't work it lets you know so you can reencode it and then pass it thru... that has been the only one so far.. my regular tv shows such as dexter, boardwalk empire, how I met your mother, house, glee, modern family, fringe, SGU, etc all have worked perfectly and only takes a few mins. I then put the files through iflicks to add the metadata and adds to itunes.