Hi Printerman,
Thank you for contacting National Instruments. Having looked at your code, I don't think that it is changing from one loop to the next. Your conditional teminal has either 0 or 1 but is wired to the While loop iteration terminal. This will go up as the program is run so I suspect the loops will go from Loop 0, Loop 1, Loop 1.... this is certainly what I have witnessed with highlight execution enabled.
If you don't want these loops to be time dependant, I would suggest that you use an Event structure. I have linked an article that explains the basic operation and I would suggest looking at the following example.
Draw Graph with Events.vi
Please let me know how you get on.
Many thanks,
Andrew McLennan
Applications Engineer
National Instruments