I was able to control the SA boxes with PDAWin TV Remote. I learned some codes into a ccf through PDAWin, and could control all my boxes using PDAWin. That ccf, using TR, would only control 1 of my boxes.

Using codes learned through TR, (into another ccf), PDAWin would only control the 1 SA box.

Using those ccfs in TR, I could only control 1 box.

It's been a while since I tested this, but if I recall correctly, I did all TR tests with and without the TR audio IR transmitter.

So it seems the iPAQ can learn and replay the codes correctly, but TR is having trouble...somewhere...but this is just a guess!