Use the Wait Until Next ms Multiple VI and encase it in a sequence structure and execute this VI after each cycle of your program completes. Main problem that you are experiencing is that you are not running your program on a deterministic Operating System. The OS you are using is multitasking events, which some events take long to process, which makes your program run long. Using the Wait Until next ms Multiple will do just that, it will wait for the next ms Multiple and then return allowing your program to complete another cycle.
John M