You've got your setup behaving very similarly to mine (7.1 Direct for DVD-A and SACD, CD for audio CD's, and DVD for DVD's - all from the same player).

My suspicion is that the auto calibration had a hard time with the sub and set it too low. A 12dB drop in the LFE track can make a significant difference. My advise is to check the following settings in the 2910's Audio Setup menu. In Audio Channel | Multichannel | Speaker Setup | Speaker Configuration, set all speakers to Large and the subwoofer to On. In Speaker Setup | Channel Level, set all channels to 0dB. In Speaker Setup | Delay Time, set all of the distances to 0ft (the 990's handling this for you so there's no need to do it twice). If you are still having trouble with the Telarc LFE test tone, go back to Speaker Setup | Channel Level and set the "SW +10dB" to On - the manual doesn't say why they would offer this, but the fact that it exists makes me suspicious. That setting isn't going to affect the 990's internal test tones, but if the sub trim is set low to begin with and the player's sub output is 10dB cool, you're going to have a real hard time getting any LFE on the player's analog outputs.