Ok ,now for the dumb question. When using the internal GPS. Do you select "Internal" or "GPS" in the configuration?
I am pretty sure that you still select GPS but I just wanted to confirm
Chosing "Internal" will turn off all sync sources and your radio is no longer looking for sync sources. Please set to "GPS" even when you don't have the enternal GPS antenna connected. "Internal" is the APs internal clock and with that it cannot synchornize with other APs.
To add to some of the information above, the GPS radio has an internal GPS chip with a patch antenna. The patch antenna is always active and is looking to recieve satellites. But once you connect the external GPS puck antenna, the internal patch antenna disables itself allowing the external puck antenna to take over. Physically removing the external puck antenna will enable the internal patch atenna again.