The problem is not clear. I do not think, that the GUI is blocked by the fact, that the display flashes.
- Do you want to reduce the flashing?Then improving the code for drawing is the most promissing strategy. Post your code if you need suggestions.
- Or do you have a problem with the accessibility of the otehr GUI elements? Then I guess, that the callback, which starts the animation, has an disabled 'Interruptible' property. See http://www.mathworks.com/help/matlab/ref/uicontrol_props.html#bqxohrx
