The car has two antennas, one in the hatch glass and the other a retractable mast. The stock radio switches between them for best reception. It's called a diversity antenna system. If you click on the Cygnus part number and scroll down you'll see it mentioned as "diver city" antenna, one of many mistranslations found in Toyota's documentation.
Anyway, if you no longer have the stock radio the odds are the glass antenna isn't even hooked up. However it can be connected with an adapter to a non-diversity receiver and it's possible a previous owner did that. It's how I've run for years. You'll need to check at the rear of the receiver to see if that's the case. More likely is you have a problem with the mast antenna, it's grounding, the cable, or the receiver itself.