This seems like one of those situations where something really basic isn't right and the deeper the "problem" gets discussed the more complex the possible solutions become.
As someone who has only been "wrenching" a couple years I had this happen more than once. I keep looking for a more complicated fix to a simple problem, usually overlooked due to lack of understanding coupled with anxiety and frustration.
I have a Carbtune and have found it reasonably easy to use and reliable. I haven't used it more than a couple times and it's been over a year. But let me ask, because I can't remember. Don't you hang it one way for some kind of bikes and the other (upside down so to speak) for other kinds of bikes? Or maybe it's a course, vs. fine adjustment? My son has an older BMW air head and I seem to recall you use the device in the opposite position for his ride vs. my 550 and 750. At the moment, the rig is at his place so I can't check it out. But I believe you can attach the hanger strap from either end.
Are you sure you have it rigged correctly?