not sure what "pyGalileo" is about. Is it on top of libmraa? If yes, could you pls share journalctl logs?
I haven't tried pyGalileo but according to your description it seems that the issue is related to it. If you prefer using Python I would use the MRAA library instead: intel-iot-devkit/mraa · GitHub
On the other hand, if you want to test the GPIO pins from shell instead of Python, I will recommend you to check this site: Intel Galileo - Programming GPIO From Linux - Malinov Family Web Presence. You will find a very well explanation about how to programming the GPIOs from Linux.