I was thinking that the A/T computer may have been sensitive to power fluctuations and that using the Alternate Flap system, drawing large amounts of current, would affect the A/T. However, it seems that most, if not all flap groups, seem to be powered by the opposite AC bus to the bus powering the A/T computer (Left AC Bus).
However, another possibility exists. The A/T computer has a Flap Lever input. According to my notes, the computer estimates the slats will move to 1 unit within 5 seconds (linearly) when the flap lever is moved to the 1 detent. It doesn't say why, but I'm guessing that the A/T commands an automatic thrust increase when this happens in anticipation of the extra drag(?). What is the normal procedure for using ALT flaps? Is the flap lever moved to match the ALT flap setting? If so, you may have a sudden unwanted increase in thrust (?) when you move the lever.
Regards.
Q.