This has been going on for quite a few versions for me but it's only bothering me now. None of the hotkeys work, main PCSX2 ones or GSDX. They didn't work on my last few reformats either. Am I missing something obvious you need to do?
I got a fresh install from the site and they work, so some option or something must have changed along the way. I'll set it up again and see if it comes back, but for now it looks like I was a bit quick in posting a thread!