@jonceramic said in Disconnected bluetooth controller causes freezes on regular intervals:
I'm assuming possible that the controller needs to be on when the system is booted under this setup so it can be discovered immediately
That's not necessary, if the pairing is ok, you can turn your controller on/off anytime. You didn't give any details about your system/controller, so it's hard to say if it's the same problem or not.
FWIW I have a 8bitdo SN30 controller that doesn't have any problems. It was updated to the latest firmware version available and I didn't have to fiddle with any bluetooth settings on the PI, it even goes into stand-by then reconnects back on a button press.