Alex, everything runs through the same transducer, which is externally mounted (as I'm sure you know). However, as I understand it, that transducer has both side and down-imaging functions and it sounds like your down-imaging function is not working properly.
I would suggest getting on bassboatcentral.com, going to the Humminbird sonar channel and asking Doug Vahrenberg for his input. He's a factory guru for Humminbird and will give you sound advice, including whether to send the unit/transducer back to the factory.