I have two exact Panasonic LCD panels mounted on a wall side-by-side. Each is hooked to a separate DirecTV box (NFL ticket -- two games at a time). I control all the equipment in my house with a pronto TSU3500.

Is there some way to change the IR signal on one of the TV so that a button press (i.e. input change, channel up) does not control both TV's?

Yes, you have to control one of them w/ a RF extender, put the IR emitter of the RF extender directed attached to one of the TVs and cover it in order to not get IR signals from the remote (that will be controling the other set via IR).

So: one set via IR from the remote control, the other one via RF.

You can also use a Xantech IR router (RT-8) behind an IR receiver but using a single extender and covering up the eye on one TV is more likely a cheaper solution.

Lyndel
The suggestion by ossocao is the method I use, works great.
Curious, though.
Have used the Xantech router, but don't see how your way would isolate any IR. It will route when different IR receivers are connected to the various routed ports, but you would still have to have the IR receivers separated somehow, which leads you back to the same problem.
BTW, the routed IR outputs are NOT amplified, like the common ones are. Found that one out the hard way! Not mentioned in the instructions and specs, even though it imply's it by it's name of Amplified IR Router.
Dan

The only way to do this is when you connect the IR bug to the TV, make sure you completely cover the IR receiver on the TV, so it will not receive any spurious signals. I believe that Lyndel meant that the Xantech solution is addressable, meaning you can select which output (emitter) any given signal goes out of.

Dave