OK a dumb question forgive me, would you verify the speaker active icons are illuminated ? There is a static icon for each speaker always present (when the speaker is set to ON), but under that static icon is another little indicator that actually says if the speaker is on or off according to the sound mode. You will see SL and SR illuminated and not just little rectangles when that channel is active.

On your question about does the cross over seem to work correctly by passsing full range sometimes yes and sometimes no, IMHO no - that implementation of a low pass filter is not correct. This should at least be documented in the manual since it's working as an as designed feature.