This is an older thread so I dont know if TheShanMan will still see this or if someone else might be able to answer.
I have the same issue and thoughts. Seems like this would be a common issue for anyone with a 4 player cabinet. I seem to never get through a session on my cabinet without hitting this combination at least once.
I thought about remapping one or the other buttons in MAME but others have to have run into this. If others have just solved this by remapping what key(s) do they use instead of the default?
However, I discovered the real solution. It occurred to me "why wouldn't that be a key mappable function just like anything else?" Sure enough, it is. Simple solution - clear the key for toggle fullscreen! Wish that occurred to me earlier! 
TheShanMan, I don't know if you'll still see this or not, but can you be more specific on how you "clear the key for toggle fullscreen?" I could be wrong but I'm not aware of any standard way built-in to Windows to accomplish this. If there is, please point me to it, or if you used a 3rd party tool to do it, can you tell me what tool that was?
Thank you.