I've seen this problem once or twice with the 100-400mm - ie. panning the aircraft, and at a certain point lens & camera stop talking. Now I thought the reason for this is that I had the camera on AF Servo and had changed the zoom while the camera was shifting focus.
I'm sure the manual advises not to change focal length while the camera is actively focusing, so I put it down to "user error". I can't recall whether or not my pan incorporated a point towards the sun, so can't say whether or not this is also a factor.
So my question is what lens are you using, and are you zooming while panning? Is the sun getting in the lens coincidental?
If you are sure it IS the sun exposure that is the problem, my best guess is that whatever program you are using, the burst of light is perhaps exceeding that program's parameters - eg. you're using TV and selected a speed of 1/100th and the burst of light causes the camera to try and set an aperture of, say f60 - I could imagine that exceeding the allowed range in certain circumstance might cause a temporary lock up.
Incidentaly I had the lastest firmware installed when I noticed this problem, so I doubt this is possible solution.
As I've only seen this occur a couple of times, and put it down to user error, I didn't worry about it - but now I will try and reproduce the problem in a controlled fashion ... if the sun ever shines again!
Colin K. Work, Pixstel