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I met stange behavior of FP of one VI: after some interactions with controls, FP locks, although VI continue to run (it can be tracked with highlight execution). It happens when I put Event Structure into SubVI (it was in VI before). And the most strange thing - FP blocks, even if SubVI with Event Structure doesn't run (just wait in memory for running).
More than likely, you have an event structure in your sub-vi waiting for action, and until you finish your sub-vi, the front panel of the main VI will appear to lockup. That's just a guess.