I had same trouble and what I ended up doing was getting the sub level quite low (-5 or -6dB) in the surround settings covering DTS/DPLIIx/DD and quite high (+10dB) in 7.1 channel analog input settings (both in Marantz SR7400). I played with DTS audio DVDs and those settings until the bass level does not depend on whether I listen in 7.1 analog mode or in DTS mode. Then I calibrated the bass level using the level knob on the sub (switching between "direct mode" with no sub and stereo with a sub - again trying to get the bass level more or less equal. Not sure how scientific this is but gives reasonable results and does not annoy me anymore.
