100% positive that my controller is fine. I use this controller for stuff all the time and it isn't even that old. It still only randomly stops working (meaning the Dpad and Left Stick since those are both tied to left/right/up/down) when I have the stuff for one of my enemy types present and actually attacking them (all but the Spawn sprite were sitting offscreen and being destroyed at start before this) but it doesn't seem tied to them since it doesn't occur during anything specific. I've gone through all the events and there's nothing tied to using the controller for movement.
Note: I remembered it breaks jumping too. Hmm, that is all platform related stuff.
Edit: It will even cut out in the middle of a jump and it is ONLY when the controller is using controls for the Platform Behavior (eg. Dpad Left is Move Left). It looks like there's a bug with the plugin, but why I am only seeing it when a certain enemy type is spawned (or has been spawned then killed or a few are still alive and just walk off the layout and fall into nothingness or whatever) makes no sense.