Has he successfully learned any codes for any product before?

When you say "our programmer" what does it mean? Is it an installer with system builder? Sales guy who is teaching himself crestron programming?

My response may be worthless to a seasoned programmer but might be valuable to the new guy.

When hes learning commands into deal he should have the remote on the table in front of the learner. Do not try and hold it in your hand. Quick taps on the buttons are better than full presses. Try and keep the timing of your quick taps the same. FYI there is a test feature in DEAL. He can move a uverse box right to his desk and test each command as he learns them.

Next thing, this is for system builder. Make sure that when he drags a command in that he changes it to 0.1s for the length of time the command needs to be sent. It defaults to "while event is active" which will typically give you problems like the ones you are describing because it sends out a continuous pulse of the command. In one case my discrete ON was turning a TV off because sending on twice looked like an OFF command to an LG. I am sure there are similar settings in simpl but i cant comment.