If you'll set a thermo on each rack, you'll notice that after an hour or two of not opening the lid, the temps will often equalize between the two racks. I've seen this many times on brisket or butt cooks. Possibly the convection effect of the round lid picks up after X amount of time. If you use sand in the waterpan, you'll often see higher temp on the bottom rack than on the top due to the radiant heat coming off the sand. But, yes, typically on shorter cook the top rack will be a bit warmer.
Just my own observations...
Keri C, smokin' on Tulsa Time