Are both of your PWM generation VIs running in the same project, or are they in different projects? If they are in different projects, check that the scan engine settings are the same in both. If it's not the scan engine, the major difference I see between the two PWM generation programs is that in one you are using extended precision math, and in the other you are using floating point and integers. I don't have a cRIO available to test, but it's possible that extended precision math is not efficient on the cRIO. Try changing it to use single or double precision,
When reading the signal, how is the scan engine configured? If it is not scanning fast enough, you won't get good data regardless of how fast the loop runs. Reading the shared variable returns the value that was most recently read; it does not force a read. You can synchronize the timed loop to the scan engine (right-click the timed loop timing options and choose Configure Input Node). There's no need to run the loop faster than the update rate of the scan engine.
