IMO it's not the 2xTC - What you have is the camera back focused slighly with the lens alone and when you put on the 2x it magnifies this defect
-> Post some pictures of a brick wall at 45 degrees angle in single-shot AF
of all the combination of lens/1.4x/2x TCs. In AI-servo it's hard to tell what the camera is predicting forward/backward based on the movements it detected either from the subject or handshake as to the camera it's just motion...
Think about it, a TC alters the lens optically and is somewhat similar to putting a diopter in front of the lens, but the camera focusing can still compensate for this optical alteration. The TC is only different in that it transfer the communications betwen the lens and the body as it sit in between
When you adjust through the viewfinder it could means that the mirror is off as well through this path!
Does this happen on both your bodies ? :idea: