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I want to use this with Steam overlay, but everytime I take a screenshot, the capture key comes up and it's annoying. I checked out the .ini's and didn't see anything about it.

How do I go about this>?

I don't think you can. Some of the PCSX2 hot keys(Save state, load, etc) can be rebound using an ini file but the GSdx specific ones such as this, can't.

Well, that is a shame. I can change the Steam screenshot hotkey, but I am loathe to do so for just one game, but we'll see.