pull off the negative battery terminal and the J19 fuse for a few minutes. That seems to "fix" a lot of problems like this with the JK. Put the fuse back in while the battery is disconnected. reconnect the cable and fire it up.
if that trick doesn't work, and you're under warranty, go to the dealership. the relay is probably sticking and needs replaced. if you are out of warranty, simply try replacing the relay.