A setting like that is probably the culprit. Most receivers allow you to individually set each speaker to 'on' or 'off' so that if you set the left/right/center/left surround/right surround to 'on' and subwoofer to 'off' you'd have a 5.0 configuration.
3/4.1 would mean 7 channels plus a subwoofer. The setting you'd need would be 3/2.1.
I would think that it is most likely a setting such that the subwoofer is shut off in the receiver, as you mention. Basically, if one has the subwoofer setting (in the receiver) to "off" or "none", it isn't going to matter what crossover frequency one selects, or whether the main speakers are set to "small" or "large", as one will get nothing from the subwoofer with it set to "off" or "none".
The auto calibration of the receiver should detect things, but if one has tried that and one still is getting no sound from the subwoofer, one should go into the manual settings. Unfortunately, the manual is not overly clear about the settings for turning speakers on and off, so it would be easier to be looking at the manual and the receiver at the same time.
As for someone's comment that the GUI (graphical user interface) is nice, it is pretty, but it does not seem to be overly clear in meaning, which makes it bad, in my opinion. I like intelligible over beauty in a GUI.
