EDIT: I've found a possible solution, posted further down, which doesn't require exiting Steam. I can't guarantee it is the best solution, but so far it seems to work without additional unexpected issues.
I haven't used PCSX2 in quite a while, and just installed and ran the most recent Nightly.
Entering a game, I found my controller (a first-party wired Xbox One controller) didn't work properly. The 'B' button paused the game, the 'Start' button brought up the PCSX2 overlay menu, another button toggled fast-forward. Instead of working as a game controller, the gamepad buttons were seemingly triggering PCSX2 hotkeys.
I spent some time in the settings menu, trying different controller configurations and looking for other options. I'd switch between SDL and D-input, restore defaults, select my gamepad, auto-assign, the displayed mappings would look correct, then I'd re-enter the game only for the gamepad buttons to trigger the same emulator hotkeys.
I searched online and found a number of posts mentioning similar controller issues in PCSX2, with various controllers, and some exactly describing the same hotkey effect.
Remembering a weird conflict I'd once had with some random free PC game I'd downloaded, I then exited Steam, which I tend to keep running in the background. I started PCSX2, went straight into a PS2 game, and the controller worked perfectly. I exited PCSX2, started Steam again, got the Steam pop-up that said it had recognized my Xbox One controller, started PCSX2 again, went back into the same PS2 game, and the gamepad buttons were again (incorrectly) acting like emulator hotkeys.
Basically, it looks like there is some kind of conflict caused by how Steam handles controllers even outside of its own games. If Steam is running, then it doesn't matter what PCSX2 appears to be telling you. I'd guess Steam is hijacking controller handling in general for Windows, and PCSX2 is getting and then using input that has already been processed by Steam, which is somehow being treated as emulator hotkeys when you go into a PS2 game?
I haven't used PCSX2 in quite a while, and just installed and ran the most recent Nightly.
Entering a game, I found my controller (a first-party wired Xbox One controller) didn't work properly. The 'B' button paused the game, the 'Start' button brought up the PCSX2 overlay menu, another button toggled fast-forward. Instead of working as a game controller, the gamepad buttons were seemingly triggering PCSX2 hotkeys.
I spent some time in the settings menu, trying different controller configurations and looking for other options. I'd switch between SDL and D-input, restore defaults, select my gamepad, auto-assign, the displayed mappings would look correct, then I'd re-enter the game only for the gamepad buttons to trigger the same emulator hotkeys.
I searched online and found a number of posts mentioning similar controller issues in PCSX2, with various controllers, and some exactly describing the same hotkey effect.
Remembering a weird conflict I'd once had with some random free PC game I'd downloaded, I then exited Steam, which I tend to keep running in the background. I started PCSX2, went straight into a PS2 game, and the controller worked perfectly. I exited PCSX2, started Steam again, got the Steam pop-up that said it had recognized my Xbox One controller, started PCSX2 again, went back into the same PS2 game, and the gamepad buttons were again (incorrectly) acting like emulator hotkeys.
Basically, it looks like there is some kind of conflict caused by how Steam handles controllers even outside of its own games. If Steam is running, then it doesn't matter what PCSX2 appears to be telling you. I'd guess Steam is hijacking controller handling in general for Windows, and PCSX2 is getting and then using input that has already been processed by Steam, which is somehow being treated as emulator hotkeys when you go into a PS2 game?