Make sure you are running TwonkyServer 6.0.2 (or later). If youâ€™re still having problems you might want to try one of these two solutions:
Solution 1: Download the â€œmkclean toolâ€ and run it on your problem files. It will fix the problem: http://www.matroska.org/downloads/mkclean.html.
Solution 2: Rip your files using an older version of MKVMerge (e.g. v3.3.0). MKVMerge 4.1 appears to have problems.