Yeah, without some way to eat up some of the volume in your MLT, a 9 lb grain bill for a 5 gallon batch will yield sporadic temperatures.
FWIW, I have a 52qt Coleman Xtreme MLT, and with smaller grain bills and 5 gallon batches, I find that my grain bed has hot and cold spots, that never seem to equalize.
I can only hypothesize that the larger amount of headspace makes it difficult for temperatures to stabilize.
I normally brew 10 gallon batches, and have no problems with temperature fluctuations, but smaller grain bills with 5 gallon batches are problematic.
Finding a way to use foam or some sort of insulation to reduce the volume of headspace would likely solve that problem, however, I have yet to try it....I seldom brew 5 gallon batches any longer.