Ummm, I didn't completely get the solution you where talking about. But I added some of your code to code which I know already does pause WMP (but not in fullframe) - and voila! It works. Now it pauses in full frame as well. I don't know how, or why, but this code below works for me.
Code:
GroupAdd,mplayer,Windows Media Player
GroupAdd,mplayer,WMPTransition
GroupAdd, wmp, Windows Media Player
GroupAdd, wmp, ahk_class WMP Skin Host
GroupAdd, wmp, ahk_class WMPTransition
GroupAdd, wmp, FullScreenTopLayout
#IfWinActive, ahk_group wmp
Space::Send ^p
Enter::Send !{Enter}
#IfWinActive
#IfWinActive,ahk_group mplayer ; All hotkeys from this point only work when media player is active
Space::Send,{Media_Play_Pause}
#Ifwinactive, ; All hotkeys from now on work in any window.
; All other hotkeys