My remote controls the TV and my laptop

If you don't plan on using the remote with your laptop, you can turn off the IR sensor in the Security Control panel.

or you could just pair each remote to their own device.

ie the remote that came with the mac, you pair that to the mac.
and pair the remote that came with the appletv to the appletv.

The newer Macbooks don't come with a remote. So, if the OP has only one....

Had the same problem with one of my laptops and the TV... I ended up going into the Applications section, the utilities, system preferences, and the library sections of the computer and deleting EVERYTHING that said Front Row.

I know it's a bit of an extreme but it did seem to do the trick. Unfortunately I noticed the IR port in the front of the computer after I had done all that. Suppose it would have been easier to just put some tape or white out over it instead. Oh well....

or disable the IR in system preferences.

what you did i would NOT recommend to anyone. quite a bizarre solution for a very simply problem.

Under the 'Security' pane in the System Prefs, there's an option to Pair a remote, as well as to disable the IR port altogether.

You found the solution that worked for you, since you had only 1 remote. I actually wanted to use 2 remotes (1 each for MBPro and ATV) and the pairing worked; now each remote controls only one device. Very simple.

And yeah, trashing all your Front Row items to get around this? Way to go nuclear on it.