Great advice. I don't think the Pronto editor offers this level of customization in terms of inverting the encoding, but I just got off the phone with Escient tech support and they suggested reversing the polarity of the serial IR cable. They say they've seen similar issues with Elan home control systems and that flipping the two wires in the IR cable solves the problem. I'll give it a try soon and let everyone know if it works.
As to adjusting the output level, I've tried this to no avail :(
