Record Enable causes Rig Input to change?

[HarrisonMK]

So, let me start by saying I'm using Logic Pro X, not Pro Tools when this happens; however, I haven't checked. It might.

I've been having problems with my rack getting stuck on the start up screen, but after restarting it a couple times it's working again. But now it only works until I try recording with it. As soon as I hit the record enable button the audio begins to cut in and out. Why? Well because for some reason hitting record enable causes my Eleven Rack to alternate between the Mic and the guitar input every second which is extremely inconvenient. If anyone has a fix I would appreciate it greatly.