What gamepad are you using? I use gamepads and have never seen this issue. What are some examples of the actions you're using? Does this apply to all actions?

I forgot to put those details.
Already tried with three diferents gamepads: wireless Xbox 360, Logitech Cordless Rumblepad 2 and a Gamecube controller using a Mayflash adapter. I use 4 shortcuts, Load and Save State, Fast forward held (this works as intended) and Toggle fullscreen.

My OS is Windows 7 64bits (tried both versións of the emu, 32b and 64b)

Another thing, every time you open the emulator its trigger any of the shortcuts with just one press, after that "first" action, it will work only with 2 presses (for each shortcut that has used the "first" press). This happens every time you close and reopen the program.
Also doesn't matter the moment of the second push to trigger the shortcut, could be immediately or several seconds latetly, even if you use other buttons between those principal actions, the shortcut always activates the moment that you press the desingned button for a 2nd time.

Alright, I'll see if I can reproduce. If so I'll schedule this for 0.9.2.

Thank you very much

Can't reproduce here with Win 10 and mGBA 0.9.1. I assigned ffwd to right-stick of XBox One Bluetooth and always works fine on first press (and next presses).

Hexaae, did you try other shortcuts? those one that doesn't work for me for example (Load and Save State, Toggle fullscreen)?.
Fast forward (held and toggle) works in my case too.
Also i was trying randomly some other shortcuts and looks like that most of them work as intended.

Results:
Pause, Frame size (2x to 8x), Bilinear filtering - Work
Reset - Doble press
Frame size 1x - Doesn't even take the gamepad, only keyboard

Ok, tested Toggle Fullscreen assigned to LSTICK press (XBox One Bluetooth) and indeed requires 2 presses to work after first press...

Sorry for losing track of this; I'd meant to look into and fix this months ago, but it slipped through the cracks until someone else reported it. I did look through the code at some point to see how it could happen though so I did get a head-start on figuring it out.