Ok I took a look into where the issues are occurring; the DVD window seems to be creating a window larger that your screen (probably bordered) and it's doing that as a child window.
But the latest version uses a borderless window if you select windowed mode. So until I have a proper fix you can try thing; go into OGLSetup.exe, set the resolution to match your monitors current resolution, and then tick "windowed".
It's not ideal but you can play the game full screen with movies. Having tracked down the cause it shouldn't be too hard to come up with a workaround with a borderless fullscreen mode.
Hi Pedro, thank you I think it will be a good compromise. I have tried to download the "Model Upgrade Pack" but the link seem dead.
I hope to found someone that can upload it again.

. Is it maybe possible, that you upload (or send me) one of your newly converted files with an AC3 stream (preferably SC_0010B). I could do the testing. If this does not work, you wouldn't need to remux all the other files unless we find a propper solution.
, and the only version of that I can find will not work with 4 (will not install as Prophecy is not installed).