This seems very odd. Here's my thinking:
- I feel like bad controls could (in theory) be a hardware problem, but you already tried a new Pi Zero. Of course our Freeplay Zero could have issues, but I can not think of any hardware problem (on our board) that could cause all buttons to stop working while other parts kept working. When you say that the USB keyboard also stops working, and that's not even something that connects to our board. Those things make me think it must be a software issue.
- If it's a software problem, we do supply the joystick driver (
https://github.com/TheFlav/mk_arcade_joystick_rpi) in our SD image. BUT, it's a kernel driver. That means that if it dies, it would likely cause a problem with the entire operating system and not just stop the controller from working. Yes, there are things that could happen to stop the controls from working and leave everything else running, but then there's the fact that the USB keyboard stops working. That's not something we control in our driver.
When you say that you hooked it up to HDMI, did you ALSO have it running on the built-in LCD?
Is it possible that the LCD stops working but the HDMI is still working? If so, that might look like no controls are working, but (in fact) the system is actually running and the LCD is just no longer responding. There are multiple things that could cause this. The LCD may not be fully seated, and it could become disconnected at random times. Then you'd have to reboot the machine to get the LCD working again.
There are, also, software things that could happen to stop the LCD driver from running. The LCD driver is not a kernel driver, so it could crash and the rest of the operating system (including HDMI output) could continue to work properly.
Try this...
Play on the handheld until it "freezes" and then (do not unplug it or reboot it) connect HDMI. Can you play it on the HDMI screen?
and also try this...
Boot up the machine and connect HDMI. Do you see the same image on HDMI and LCD? Start playing until the machine freezes. Is it only the LCD that froze? Is HDMI still working?