Everything works perfectly with my first navio2 drone, but the GPS. I didn’t have any problem with wiring.
I removed all parts which I suspect that may interfere the GPS, reflashed the SD card with 20160408.img, placed the board on the field with open sky view for 15min, but still there was only one satellite found according to u-center.
RPI camera is known for interfering with the GPS, so it might be the case. Could you try to swap the antennas with your second set to see if it might be faulty?
I also noticed that the antenna quality is very inhomogeneous. One antenna can barely find a lock at an open field. Another one works inside my apartment withing seconds.