My guess is that the speakers are not set to small, so the sub is only seeing information from the dedicated LFE channel on discrete surround soundtracks.

Double check that all channels are set to small, and see if there are distinct settings for the various soundfield modes. Maybe the pre-pro wants to default the stereo (and multi-channel stereo) to 2.0 full range and your LFE+LR only applies to the surround modes unless you dig into the menu somehow.