Ok... These are quadrature encoders. Each one has two signal wires producing a dual square wave at 50% offset. Which one is first is dependent on which way the encoder is rotating. I am only using one signal wire from each encoder. There will be three. Right now there are only two... Elevation and Azimuth. I have the chip and BT module inside on my breadboard temporarily. The encoders DID join outside onto one wire, but due to growing concerns as to what happens when the unused encoder is in an "other than floating" position, I separated them all the way to the breadboard. They still go into the PIC on just one leg, but are physically separated by a SPDT relay now. I will re-code and put them to their own leg in the end, but at the moment, the relay seems sufficient to separate them so as to eliminate that as the cause of this problem.

It's really baffling to me how I can be looking at the exact same pattern on the scope, and yet the PIC is reading an ENTIRELY different thing. To go from ~7500 pulses from end to end, all the way to 300,000 to 400,000 pulses would cause a MAJOR difference that I just couldn't mistake on the scope, and it's just not the case... it looks like no change at all, but the number count is insanely different.