My controls are suddenly all over the place, any idea how to fix this?

[ShozanM]

So, until yesterday, everything was fine with my controller, all the controls were exactly as expected and I was using RT to pause the emulator (which is also Escape on the keyboard by default) and LT to accelerate time.
But then suddenly there was changes in how the controls work (without any of my input, it just started happening when I launched the emulator yesterday).
Now, the Start button on my controller pauses the emulator juste like RT did, and Select does the time acceleration, and B (on the xbox controller) does the same thing as Start did before.
I've tried to remap all the controls manually, or even delete all the controls associated to the Start button for example, but it doesn't change anything, pushing Start still pauses the emulator. It's like all the controls got rewired in a very bizarre way and I don't have any control over it.

Any idea where that comes from? The controller works totally fine on my other games on Steam, it's just the PPSSPP emulator.