The other thing is we noticed as you track a radial of the VOR or an NDB homing to the aid is that you have to ignore the CDI deviation of the GPS as it will change wrt ARP especially in case where VOR is sited at a different point on the AD.
Don't set the airport as the destination in the GPS, but instead set the ground based aid and you wont have that problem, just make sure you set the right one.