Hi tobiasbp,
Well, you should manage to find a horizontal frequency setting where PCB, Groovy's menu (gasetup) and games are all synced. It probably requires just a very subtle adjustment to achieve it. Bear in mind that all three frequencies are very close, and the monitor will have a range of tolerance, you just need to move the potentiometer a bit so these three frequencies fall inside.
As for the size/centering, you're right, you'll need different adjustments when you switch to the PCB, but you can also find custom software settings that reproduce your PCB borders size, if that's what you like (this won't apply to gasetup anyway).