A solution to this problem, though apparently only a partial solution, has been found. Please see a post by idefix44 here:
http://www.mission4today.com/index.p...sh=15&start=15
Turning off the "24 bit user skins" in the Difficulty menu, per idefix44's suggestion, does seem only a partial fix. The click/Ctrl delay in setting objects and waypoints in the FMB is reduced to a fraction of a second, but the lag is still perceptible, and still a mystery.