Apparently the service manager is unfamiliar with how electronic connections (whether at the connecting end or in the cable itself) can go in and out for many reasons. Short in the cable somewhere, bad connectors at either end (or both ends), a defective receiver (the antenna itself). All of these could cause spotty connection, or it could cause the connection to go out completely. But it's most certainly not a 100% on or off case.
Honestly, if you have access to another dealer I'd go there and explain the situation. Original dealer replaced the headunit, but refuses to even consider that the (still occurring) problem may be with the antenna.
If you feel like tinkering (and electronics warranty is up or almost up) you could always look into replacing the antenna yourself.