LabVIEW uses dataflow to determine which part of the diagram executes next. The outer while loop will execute the Cont sample VI once and then start the inner while loop. The for loop will run until all the data has been written to the digital line. The Trigger and Gate2 VI will execute (maybe before the for loop). If a data point was available, the inner loop will continue by executing the for loop again with the same data. The time for the execution of the inner while loop depends largely on the size of the data arrays. If the boolean data to the for loop has 100 points, each iteration will take a tenth of a second. If there are 20 valid triggers in the waveform data, it will be more than 2 seconds before the next iteration of the outer loop.
The 6008 is a rather slow device and is generally not suitable for PWM work. If your requirements are tolerant enough of the slow speeds, then you will want to modify your program for parallel operation of the analog input and the digital outputs. This means that each part will be in a loop of its own without data dependency between the loops.
Lynn
