Phil,
The difference in delay between the "IFI" PWMs and "Kevin's" is because PWMs 1-12 are generated by the master processor, while PWMs 13-16 are generated by the user processor. The master processor PWMs will only occur after the communication has taken place between the two (roughly every 26.2 milliseconds), while the user processor PWMs are generated immediately. More details about this delay can be found
here.
Mike