In the speaker configuration menu, pg 72 of the owner's manual, make sure the crossover points are set to 80Hz. Make sure this setting is not at "full range" or all your bass will go to the main speakers and not the sub. Once you set this to 80Hz, all the frequencies below that point will go to the sub, even in stereo.
The LFE channel is separate and always goes to the sub anyway, so this would explain why the sub works when an LFE signal is present, but not in 2 channel stereo, at least in how I interpret the owner's manual.