If you have the fig file open in GUIDE and click the run icon (the green triangle icon) then it will run just the same as if you had typed F5 or clicked the green triangle icon in the text editor in MATLAB.
If you try to run it by double-clicking the .fig file in the "Current Folder" panel in MATLAB, then I've heard that you will have problems. (I never do it that way so I don't know but everyone says so.)
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