Yeah, Its rather strange as they both should be able to coexist but as you say, only one can hold the candle it seems.
My rather dirty script where it puts MAMEHooker up in the food chain just before launch works great, just that you need to do this per game
and that its not that optimal having old killed icons down the right besides the clock for each operation killing and reopening the MAMEhooker app.
Do you know how to remove a stray icon after you kill its process btw? just to keep things tidy