Are you using the latest version of CoreAVC? If I remember it correctly, there were some issues with MediaProtal and CoreAVC a while back (at least I know it displayed this behaviour with .ts files).
You migt also want to try the latest SVN version (or wait for 1.0 RC1, which should be out very soon).
Sounds like the bug of CoreAVC that was fixed with 1.5.1 (or was it 1.5.0?)
You should have received a link from CoreAVC to download the latest version.