I confirmed that if you disable the USB A Host function in the prefs.csv file, it will start up OK with the pull up resistors.
If the host is enabled, and the input lines are pulled up, it thinks there is a device plugged into the A port and it tries to talk to it. You can see the blue leds go through their pattern and then everything stops and the program hangs. Eventually it reboots in an attempt to recover.
Adding the "enable_usb_a_host,0" line to the prefs.csv file will prevent that and you can use those two inputs. I've attached a prefs.csv file with that line in it. You can just copy it into your quadstick's flash. Any preference changes you have made to the default preferences will need to be re-entered.