I Assume you're using the Set Control Value method, and it works before you run the VI.
Discarding the obvuious answers (wrong name\data\type descriptor...) I can think of 2 reasons why it won't work after you start:
1. You are trying to set a boolean control with a latch action, or the inner VI is changing the value back from its code.
2. You've set the Run VI method to Wait until done, meaning the code of your top VI will stop running and wait until the subVI finishes. If this is so, just set it to F.
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