With the fronts set to large, two-channel sources played back in stereo should have no subwoofer present. Obviously if a surround mode like PLIIx is used, that changes things.

I'm starting to wonder if you don't have some room problems - the fact that you get "boom" and/or start having problems integrating sub and speakers as soon as the sub starts reproducing anything about 40hz really seems out of place. My SVS 25-31PCi gave me a little grief in this regard at our old house (crossed fronts at 40Hz so the sub wouldn't intrude when listening to music in two-channel), but it was better behaved in our new house (although the LFM-1 blended better still, as I mentioned in my LFM-1 review) and it wasn't as bad as what you are describing. You're just having way too much trouble getting the sub to play nicely with the rest of the system, and the most likely explanation at this point is room effects. Fixing it acoustically (sub placement, bass traps, and other acoustical treatments) is an ideal approach, but it's tricky business. You might actually want to consider something like an SMS-1 at this point (in which case I strongly recommend Outlaw's SMS-1 Guide to walk you through setting it up optimally).