[Gabeloooooo]

Is it really popping up in a window where you can't use the remote? If it is, something is very wrong.

If you really want to chase this, download and install graphstudionext (https://code.google.com/p/graph-studio-next/ and the Windows SDK and register proppage.dll (Instructions for this part here).

Then while playing the video, 'attach' to the running graph and screenshot the graph and post here.

Alternatively, setup vlc or mpc-hc as an external player (see the wiki) and when you want to play one of those problem videos, when the title is highlighted in XBMC, press C and then select Play using and chose your external player.

Thank you! You've given me many things to investigate. The second I've time to (code for when the kids decide to sleep hehehe), I'll try all of this and report back.