I can't help with missing VI's.
I would recommend that you consider a state machine architecture. Set up an initialize state, and idle state, start state, running state, stop state.
As you have it now, the inner while loop is doing nothing. It just runs once. All of the iterations are occuring on the outer while loop. Some subVI's are executing on every iteration such as Configure Vector space, Load Position, Start. Which I don't think you would want executing on every iteration.
Another oddity is that those subVI's look like they would have a .flx extension rather than a .vi extension.
Two more tips.
1. You are forced to abort your program to stop it because you have a false wired to the stop terminal of the bottom most loop. So it would execute forever.
2. In the middle loop, if you change the stop condition from Run while true to Stop while true, you could get rid of the Not function leading into it.
