Before I could even be able to begin advising you on the issue you are asking about, there are major structural problems in your code. The block diagram is huge - and that is NOT a Good Thing. It is also very difficult to read due to the colorization of the structures. Green scalar boolean wires are very difficult to see on a blue background. My sense is that you started coloring things because you were getting lost on the diagram.
The solution is modularization - creating small, reusable routines (subVIs). The required functionality for these subVIs will become apparent through as you decompose the application's functionality into its constituent components, sub-components, sub-sub-components, etc.
Also be sure to utilize dataflow to manage the execution of the code, not artificial structures like sequences, and connect up the error handling. Your application can't tell you its broken if there is no error handling.
Mike...