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No matter what options I choose from the launch thingy, Pop 2 is extremely slow on fullscreen (I'm talking single figure frame rate). Is there a way to improve it or is this normal?
But it runs just fine windowed?

I'd upgrade your video card drivers just in case. What type of CPU & video card do you have anyway?
I have the same issue. On a new macbook pro. For me it's when I switch to fullscreen within the game, it has it's own fullscreen mode as well as the emulators fullscreen mode.

Any tips on how to solve this would be very welcome.