Hi David,
I believe you are mistaken.
The confusion is probably due to differing nomenclature:
In Paparazzi a negative pulse_type means that it will trigger on the falling flank, positive on the rising.
So with a positive pulse type, the positive part of the signal carries the PPM timing pulse (inverted PPM modulation)
However, a negative pulse type is apparently sometimes also referred to as positive PPM modulation (I guess because it looks like as if you have short positive/high pulses and otherwise low signal).
Also this is probably sometimes confused whether the carrier frequency and positive/negative SHIFT marks the start of the pulse (in FM transmission). So whether carrier PLUS shift is mark(on) or carrier MINUS shift is mark(on).
So I'm pretty sure that the example radio files and the wiki is correct, but if there are still some files with wrong pulse type don't hesitate to report that so we can fix it.
Cheers, Felix
P.S. Where did you have problems? Futaba radios should be correct with positive pulse type....