Hey Danny,
Sounds like maybe a signal ground problem. Reading thru the NSEQ manual, it says that Pin 1 is tied to chassis ground, Pin 2 is hot, and Pin 3 is tied to audio ground.
If there's any difference of potential in your system between chassis and audio ground on one side, I think this could account for a level mismatch... I would take a multimeter and check your patchbay. Set it for continuity test, unplug your audio cables, and make sure you have continuity between all pins (1 to 1, 2 to 2, etc). If you're missing continuity on any of them, that's a possible problem. Once you've assessed that, then check from the patch bay to the cables at the back of the NSEQ.
If you get the dip in level only after plugging in the other channel, it could be you have a floating ground on one side, and the other pulls the ground up (reducing hot-ground potential, and thus level).
My understanding of this is cursory, and might be inaccurate, so take it with a grain of salt.
But do check all your pins and cables with the multimeter.