If the problem follows the file to a different copy or computer, then the VI is probably corrupt. Typically, the best course of action with corrupt files is to revert to a previous version of the file and continue development from there.
There is no one correct way to code. However, there are general best practices that should be taken into consideration. For the Clean Up Diagram button, it is not suggested to use on large VIs. In general, it should be used on small sections of code, and used throughout development if at all. It is meant to optimize the visual appearance of the Block Diagram, so it is not necessary to use.
In order to avoid VIs that take up multiple monitors of visual space, among other reasons, it is suggested to break parts of code into subVIs. These are especially useful if there are sections of code that are repeated.
It is also good practice to have some method of dataflow to determine the order of execution. Without any dataflow control, the Clean Up Diagram button will stack all of the code vertically, signifying to run everything in the stack at once.
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