That receiver has some strange modes, such as "compressed music enhancer" and "high resolution music enhancer". Poring over specs and reviews I don't see a simple "stereo with sub", so I guess you have to use one of those two and shut off a lot of "extra features" to get simple 2.1 channel music for an analog source.
If my assumption is right it's defaulting to Pure Direct mode for analog 2-channel input. To get the sub working it has to send that signal through the receiver's DSP section.
EDIT: Looks like the only way to get it is to toggle through the stereo modes button on the remote by repeatedly pressing that button.