I ended up building a complete new htpc, installed a new windows 7 installation, and used the latest stable build of mediaportal and the problem went away lol. Not really a fix you are looking for
Marcel, I see you're using LAV Video Decoder. What you could try is the following:
Open LAV Video Config, select tab 'Formats' and UNcheck the bottom checkbox (Use Microsoft WMV9 decoder for WMV3 and VC-1).
That might fix some issues.