i had the same problem when i got the Thunderbolt display to put next to my iMac. its literally like 3/4" to low to have the sides match up. I got a piece of wood and sanded it down and and stained it and its perfect now.
Did you hook up the Thunderbolt display to a 27" iMac?
I would not expect the Thunderbolt display to be lower than an iMac, since they're both Apple.
I'm thinking of getting hold of a block of wood to make it a bit taller. I'll probably do that once I get hold of the new desk though.