So what would happen if I separated it from the mix entirely?
Please don't take this the wrong way...
but Give It A Shot! :-) Hit that "Bypass" button before driving up the system next time you use it, assuming you want to preserve the settings, or if you don't care about the current settings, reduce all of the settings to zero-impact-on-the-system. Give it a listen to see how it is. You might find that other "weirdness" raises their heads once this is removed, but finding *those* things and dealing with them will go a long way to making you happier in the long run!
Side note: where are you located? If you post your location, there might be a LAB member close to you. Often, for the price of a pizza and a six pack of beer, you can get someone to swing by on their day off and give you a couple pointers!
-Ray