Y Axis reversed

[Jotaro Kujo]

So, I just redownloaded PPSSPP because I remember how good it was despite emulating a rather recent system (it runs faster than a DS emulator on my PC), but, when I was remapping the controls to work with my gamepad (a 3rd-party PS3 controller), I tested the analog stick, and the Y-Axis input was reversed (up made the marker go down, and down made it go up).
So I think, "oh well, guess I'll just map down to up and up to down", so I do that, and test the analog again.
And, input is still reversed. Down still goes up, and up still goes down.
Has this happened before, and is there a fix or workaround?