Remember you have the same issue with the 70-200 f/2.8 combination as well... (with the same body???)
I've noticed the same problem with the 2x TC on the Sigma 70-200mm f2.8 and I'm trying to get to the bottom of it.
-> A TC/lens combo does not do the focusing. The AF phase detector below the mirror chamber looks through the resulting TC/lens combo and the camera based on this detector reading sends the appropriate commands back and forth to the lens so that the subject comes into focus @ the AF phase detector (and not neccessary the CMOS sensor
as the mirror is in the path while focusing).
This mirror/sub-mirror assembly can be slighly out of alignement (i.e. not exactly @ 45 degree) and the whole deal is off. This mirror folds out of the way for every shot so it's one of the the most frequent moving part in the whole system (some camera can flip this mirror assembly 10 times a second!) so it's not very hard for it to be slighly off at rest with all this banging going on...