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Have you verified that lens/TC/camera contacts are clean and properly connected (solidly "clicked")? Also, what version of the 2X TC did you use? Can you post a picture with EXIF intact so we can see exposure settings? Shot handheld or tripod mounted? Was IS on/off? AI Servo or One-shot?
I would also try to mount the rig on a solid tripod and gimbal head, pick a contrasty subject, and take some shots using both PDAF and Live View CDAF, using center point,
One-Shot AF. Check for any inconsistency in the focus between PDAF and CDAF results. I have used FoCal and gotten inconsistent results from time to time. You might consider trying Dot Tune as a way of double checking FoCal's results.
Hope this can get you going in the right direction.