Help My Rel has gone berserk

Hopefully I'm just being thick and someone here can point out my stupidity. I have a Rel Storm III which I use for 2-channel as well as home theater. It is hooked up via rca interconnects (a y-connector) to the low level inputs on the Rel from the sub out on my home theater processor. I have the Rel in mode 2, to bypass the filters on low level input (since this is the .1 in a 5.1 from my processor). I have the left and right channels of my stereo amp hooked up to the high level input on the rel via the neutrik connector. Here's the thing - the high level volume control doesn't affect the volume of the bass on 2-channel. The low-level volume control certainly does affect the bass on surround sound, as it should, but it also affects the bass on 2-channel, even when my surround sound processor is off (which it shouldn't, right?). So, when I have the bass turned up high enough to make an impact on movies, it's really loud and muddy when I listen to 2-channel. Again, high-level volume control appears to do nothing at all. Help! -Dave