Controller config is broken

So, I can't get any version of epsxe to work on linux. The linux version is FUBAR, runs too fast, and sound is all garbled, plus gamepad is borked completely. So I use the Windows version in Wine, and the only thing that doesn't work, is the controller. Now months ago, it USED to work just fine, but now it simply dosen't. When I click on a button to map, it automatically is assigned an unrelated input (like J3_left), and when I hit the correct button, it jumps right back to the incorrect input, as if a button somewhere is being continuously pressed somewhere else. No idea whats going on.

go to assign a button.
Press the button you want and do not let go of it.
click the next assignment and then let go of the button
repeat.

Seems the button only registers if its held down and the focus to the input box is lost. Same with Windows.