Found this out when I updated my Mediacoder. The new version installs a new version of MKVmerge and it has a new trick my Mediainfo called it header stripping and mediaportal will not play MKVs with this. If this happens two ways to fix this if you dont a version of MKVmerge before 4.0 I think I have 3.3.0 download one and run the file trough it it will remove the header stippping. if using new version of Mediacoder then delete the file MKVmerge.exe in mediacoder and copy the old version in its place and everything will now work again!