Don't have one of these myself, but you could check the following.
Some units allow you to store separate levels/settings for the different formats. When you calibrated the unit for DD you would have set an LFE level. Maybe you also need to calibrate the DTS side of things separately. Try switching to DTS and then perform the setup process for the channel levels, see if this helps.
Also I understand this unit has a fairly comprehensive bass setup menu. Perhaps some tweaking here is in order.