As it cant make contact on the camera, I feel they may be connected up on a test-bench in a Canon repair center. I speculate it may be to program the lens...
I recommend some additional speculation...

What's different about your 100-400 from your 24-105 and 40/2.8? The OP mentioned 'extra' contacts on a 70-200/4 IS. What do those two lenses have in common, that lenses like the 24-105 and 40/2.8 don't? Hint: you'll find 'extra' contacts on L-series prime lenses of 135mm or longer and L-series zooms of 70mm and longer, except the 70-300L.
The 'extra' contacts are for communication with teleconverters, so they are found on lenses that are compatible with Canon extenders (and also on the 50mm compact macro, for communication with the life size adapter).