Oh wait a minute, DistortedTJ's question reminded me of something... is this hard top new to you and your TJ originally came with a soft top from the factory? If so, you'll need the hard top style rear brackets, the two that are screwed onto the tub on either side of the tailgate. They have a slightly different dimension than the brackets that come with the soft top. The hard top brackets will work ok with the soft top, just not the other way around.
Edit: If that's the case, let's trade brackets since I no longer have my hard top and would like to have the soft top style brackets back onto my TJ.