I had two While Loops altogether, Trigger Event Loop and DAQ/Shift Reg Loop. Thinking that there was something wrong with the DAQ part, I made that into a separate Loop. The problem stayed in the Shift Reg Loop.
The new DAQ Loop and Trigger Event Loop were not even iterating, Therefore I assumed the problem resided in the Shift Reg Loop.
After reading of similar problems in the NI Discussion Forums, indications were pointing to memory problems that were describing my actual problem.
Solutions were to either use occurrences or only open the front panel when running the program without viewing the diagram, this solution reduces the amount of memory required which worked. However I could not see the effect of applying any changes to the diagram easily.
After reading "architectures_for_designing_labview_applications.PDF", it was suggested to make Local Variables in each Loop.
Utilizing the information found I looked at the way my loops were being stopped. They were being stopped by Property Nodes via a Boolean Indicator, which the other Loops were using to stop.
No Local Variables were in the other Loops.
So I rebuilt the stop sequence, removed the Boolean Indicator and made the new Stop Button with Local Variables in every Loop.
Everything worked?