My first suggestion would be to follow up the auto setup with some manual adjustment of the sub, as sub calibration can be quirky. If you have an SPL meter, run the sub's manual test tone and see what the meter gives you. Also try a few bass-heavy demos (depth charges in U-571, Darla tapping the fish tank in Finding Nemo, and any of the other common bass-heavy scenes). Most people end up adjusting the subwoofer level "to taste" and I wouldn't be afraid to do the same.

Telarc's suggestion about disconnecting the sub cable is pretty odd - presumably their 1812 SACD is mixed as 5.0 if they are doing that, and they're assuming that the bass management is happening at the receiver or processor (which is rare with SACD). Without digging deeper into how the disc is mixed, I can't really condone their suggestion even for a single specific case.

I do have a couple questions about your setup. First, I assume that you are handling all of your bass management in a single place - meaning that you have either set the 2910 to do no bass management (all speakers large and sub on) or the 990 to do no bass management (all speakesr large and sub on). If you have small speakers set in both places, you are applying bass management twice and the crossovers will be overlapping. Of the two options, I would tend to recommend that you set the speakers to large at the 2910. Also, are you using the multichannel analog connection for regular DVD's as well, or just for DVD-A and SACD? As a general rule, I recommend using the digital output for DVD's even when the DVD player supports Dolby Digital and DTS decoding. For one thing, the 990 has the more robust bass management. For another thing, the 990's Pro Logic II processing is probably better tweaked and refined (not to mention easier to control), so Dolby 2.0 discs will yield better surround sound if the 990 does the processing than if the player does it. Lastly, the 2910 cannot provide Dolby Digital EX, DTS ES, or Pro Logic IIx decoding or processing. Not all of these matter to everyone (if a global 80Hz crossover works the better bass management isn't a big deal, and if you only have a 5.1 system the EX/ES/IIx modes aren't relevent), but in most systems at least one of these will apply.