Any idea what does this tool actually do?? Because, the file which it gave as an output has exactly the same size as the problematic one, but still plays perfectly on the Mede8er after it got processed by the tool?
Imagine turning on a DVB TV and tuning to program which has already started, only to be told you had to wait for the start of the next broadcast to catch the header containing codec information about how it's encoded. This situation dosn't happen becuase the header is repeated at reguler intervals through the stream. All that MKV Header compressions does is treat a stream like an ordinary media file by removing the header from the stream leaving just the header at the beginning. The header isn't that big, so repeating it at intervals dosn't increase a file by much. Conversly, removing it dosn't decrease a file by much either, making the whole idea of MKV Header Compression rather pointless.
Supporting MKV compression in version V4beta dosn't mean tuning the codec chip in the med so that it can play non complient streams which don't have the distributed header. It actually means programming the support processor to re-distribute the header thus creating complient streams the media chip can play. That is what the software tool does to a file if you use it to remove MKV Header Compression.
It's all a pointless exercise driven by MKV zealots who aren't responsible to any industry body.
Those having problems with normal solution to fix it could try this instead:-http://www.digital-digest.com/software/PopCorn_MKV_ReMuxer.html