I've played a few times to check this out. It only happens when I have alot of units (60+) and tends to get worse as more units are added. It could be something about my system configuration. Since we have such a small test group its possible that it won't happen on other systems. It might also be down to a graphics problem similar to the building placement bug in Glest which only occurred on some systems.
EDIT:
Good news (sort of), this isn't a GAE bug. It also happens with Glest 3.1.2, although slightly less pronounced. I have found that it is not clicking units which is the problem but ANY left clicking and also drawing boxes with left click. When GAE is running at its top frame rate one click will cause a small skip, repeated left clicking will slow the game down to single figure frames!!
Please don't waste too much time on this since I am almost certain that it is related to my system and in paticular openGL.