This issue is not uncommon for Sync 3 swaps using aftermarket GPS antennas. This thread has a lot of info about GPS signal and issues.
No GPS signal after updating from 3.2.18124 to 3.4.21098 - Ford / Sync 3 - CyanLabs Official Community
Here is a troubleshooting guide for the GPS antenna.
PINPOINT TEST T - Compass or Navigation is Inoperative.pdf (638.2 KB)