Your last message about using a Xantech emitter throws me a little. Does your original remote still work ok from a distance?
I programmed a TS2000 about 2 years ago that I struggled with using a Mit. HR..XX The Pronto would acknowledge it had learned ok, but it would never work .. After about 3 tries like this I was about to give up.... Then I turned off the lights, you read it correctly! Tried learning again and this time it worked (works) great. This has been the only manufacturer I have had to resort to turning the lights off with to learn codes. I have programmed about 30 pronto's since then. Also I have run into a problem in a board room that is using fluorescent fixtures and using a Pronto remote. We also used the Pronto to control these dimmable fluorescent fixtures and as long as they were not at 100% my remote worked fine... Ramp it to 100% and the only way I had control was to stand between the lights and 2 feet in front of ir sensor.