Same issue here. FLStudio 12 and z3ta+ 2.1
As long as the joystick is enabled, you can't use the "browse parameters" function in FL Studio. The MIDI input display in FL Studio shows the joystick value all the time, it seems that there is constantly some kind of input which blocks access to other controls.
You even cannot disable the joystick permanently. As soon as you close and reload a song in FL Studio, the joystick is enabled again. And now imagine using several instances of z3ta+... really annoying.