Matt,
My memory of this is several years old, but if I recall the embedded code correctly, the first cycle will always be accurate. The last cycle may or may not be accurate depending upon the conditions (as follows). The cycle will be accurate if the new width is written during the low period of the cycle. If the pulse is active (Hi) when the new width is written, and the new pulse width is longer than the old width, the cycle will be accurate to the new width. If the new width is shorter than the old width and the new width time has not yet elapsed, the cycle time will be accurate to the new width time. If the new width is shorter than the old width, and the new width time has already elapsed in this cycle, the signal will deactivated giving a single pulse width that is between the old width and new width.
This should be fairly easy to verify with a FP-PWM-520 and an oscilliscope. Set the period to a relatively long time, (e.g. 10 seconds), and watch the response as you change the settings. With a 50% duty cycle on a 10 second period, it should be pretty easy to send the change during both the Hi and Lo periods.
Regards,
Aaron
LabVIEW Champion, CLA, CPI