I believe that this is normal using Media Player. When in full screen it's not active ("in focus") to recieve the commands from the remote.
As an example, when you press the pause button on the remote:
- It first checks which program is "in focus" (active in the foreground) to see if it's compatible (or has a plug-in installed for that software).
- If it sees that Media Player is running in the foreground, the remote simulates pressing CTRL-P on the keyboard (which is the keyboard shortcut for pause).
Because of the way that Media Player works in full screen mode (it actually works as a background app and isn't in the foreground), the remote doesn't know that it's open and doesn't send a command.
I suppose that the remote software was designed that way so that if you have something like Internet Explorer open, accidentally pressing the pause button doesn't begin printing a webpage (CTRL-P is the keyboard shortcut for Print).
I know that you can assign on the of remote keys to simulate the ESC key, which would take Media Player out of full-screen mode so that the Play/Pause/etc works. If I could figure out a way to assign ALT-ENTER to a button to go back into full screen I'd be a happy camper.
I usually use PowerDVD (and plug-in) to play files now, since it does everything that I need to do and is fully functional in full screen.