A friend of mine had this problem, and we made an AutoHotkey script to run as part of the 'pre-emulator' program.
Autohotkey is nifty, because it lets you make small scripts that you can actually run as exe files.
What he ended up doing was making a script that, when mamewah opened a game, first ran this program, then ran the game. It waited for about half a second, then put focus on winvice (instead of on the unzip.exe). Then, he made another script that 'killed' the first one for when you closed the emulator in mamewah (to prevent 40000000 copies of the script running on your computer).
I'm trying to remember how it went, but I think the ahk script was something like:
sleep, 1000
Controlfocus, Winvice (or whatever the title of the window/process is)
and the killscript was:
Process, close, WinviceHelper.exe
Check out autohotkey if you can... it's free, and can do just about anything from joystick-to-keyboard mapping to advanced things like keyboard/mouse macros. It's awesome for cab software, and a great compliment to frontends since not all emulators allow for easy configuring of controls/functions.
http://www.autohotkey.com/Fiddle around with it a bit, and use my advice, and I'm sure you can create two tiny scripts that get the effect you want in no time.