I guess the RC-9500 doesn't understand 900A form and Wizz-it compensates by translating the signal to the form all models understand.

The differences between the way it translated and the way I translated shouldn't matter. Doesn't the code I translated have the same problem as the code it translated?

As for the problem itself, I'm not sure what aspect of the signal timing is causing that failure.

What do you mean by limiting the burst? I didn't know there was any feature like that in a Pronto.

The two values in that Pronto Hex string that control the timing are the two large ones near and at the end (0795 and 0E55 in the one Wizz-it translated). I think increasing those, especially the first one, might fix the problem of double signals. But maybe things are behaving strangely and decreasing them would help. Only big changes to those values can have a noticible effect, but I'm not sure of the max that the RC-9500 can understand. Try changing the 0795 to 0F00. Try changing it to 1800.