I'm assuming that the position source part was set to Furuno BB GPS, correct? If it was and the GPS Sensor selection under memory clear wouldn't allow the EDIT button to change it to YES, then the NN2 is not "seeing" the BBWGPS. Most likely the BBWGPS is bad and needs replacement. If the GPS receiver is mounted on the same horizontal plane as the radar or within the radar beamwidth (approx. 22 degrees from the vertical center of dome), then the radar most likely damaged the GPS front-end receiver. This is because the radar transmits RF and the GPS receives RF...if the radar is transmitting directly into the GPS, it's receiving too much RF which damages the receiver.
As for the start-up check message, normally that means that the backup setting data is missing. This usually occurs after a factory clear of the display has been done or the backup battery has failed. There would have been an indication if the battery was going bad, so it's most likely that the display got cleared. You can verify by checking for your waypoints...if they are gone, then someone pressed the clear or alarm button during the power up process. Once the settings are accomplished again, that fail message will go away on the next power up.