One thing to check is when you program you are HOLDING the original remote's button down until the Pronto finishes. It will sense a repeating signal and only store it once, with the repeat command.

If you're just PRESSING it you may send the signal two and a half times, and the Pronto will store it two and a half times - taking up more room. From what I've seen there is no way you should run out of memory at such an early stage.