I'm not sure this helps or hurts, but in my 950, the analogue crossover (attached to the 6-ch analogue inputs) inverts the summed LFE output when it is engaged.

I run the subwoofer signal from the 950 through a Behringer DCX2496 which does equalization. It also has a one-touch phase inversion function on each channel. When I listen to CD through coaxial digital input or 2-ch SACD through the 2 channel analogue inputs, I keep the phase normal. When running SACD surround through the 6 channel bypass I invert the subwoofer signal.

I'm not sure why it's implemented this way either, but at no time do I have to adjust the sub level. Is it possible this is what you're seeing? If the sub is inverted and fighting with your mains, it may seem like you need to boost the sub level.