I have been experiencing that exact problem. I read on another thread to try deleting the problem button, download, then add the button again and re-learn. Although that moved the problem around to other buttons, I still had the same problems when trying to learn commands from an RCA remote for DirecTV.

I even tried deleting all of the buttons on the page and then adding them back with no success.

I purchased my remote from Crutchfield as well and would be curious if the new unit solves the issue. If not, I guess I figure out what the next best choice is.