If there was something wrong with the 6.250 software update, installing another version could correct this. I would check the connections first and be very, very careful if you decide to bend any pins on the GPS Receiver connector.
I would also try removing the black plastic cap at the end of the NMEA “pigtail” wire (this is the second shorter wire that comes out of the GPS Receiver’s connector). Make sure that none of these wires is shorting out to each other. Reseal this when you are done.