I do not have IMAQ so I cannot run the VI.
1. How are you testing the "time to operate"? The booleans are read almost immediately when the VI starts and never read again so any changes have no effect. Are you using Run Continuously? That is not intended for repeating the operation of code - it is a limited use troubleshooting tool. If the code should run multiple times place a while loop around the code and add a front panel stop button to end the run.
2. Except for the file paths and the indicators it appears that the code in each frame of the sequence structure is identical. Create an array of the file paths and put the code inside a for loop. Much cleaner, no hidden code, and can be expanded to any number of files just by adding elements to the path array.
3. How long does the code in the sequence structure take to run? Even though the case structures are parallel, the entire VI can only repeat after everything has completed. Perhaps you need two while loops, one for the code controlled by each boolean. Look at the Producer/Consumer Design Pattern for an example of parallel loops. That pattern is somewhat more complicated than you need, but you can see how parallel loops can be used.
Lynn
