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?

works for me

but then, you didn't mention anything about your system.

VBA-M

I literally can't think of anything to do with my system that would cause this so I figure a better approach is to think about what could cause them to not work.

Anyone?

Post a screenshot of your lilypad configuration screen (keys and general tab)

Here is the config.

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!

Try unchecking use GS thread. If that doesn't work also try unchecking monitor when in background

No combination of those options changes anything. A fresh PCSX2 install with the same settings doesn't have these problems so I don't know what broke it.