This happens when you're clicking on Swing elements faster than they can be rendered (for example, JTree nodes that need to expand/collapse as I suspect is the case in your case - right?). The fix is simply to use the EDT instead of accessing the JComponents directly from the main Matlab thread. If you have R2008+ then simply use the javaObjectEDT function after creating each Java object instance.
Yair Altman
No - it means you'll need to use awkcreate/awtinvoke for all your GUI instances (my sympathies...). You can use programmatic pause() statements in strategic places as a poor-man's alternative but it will only reduce the problem, not dismiss it altogether as using the awt* functions. Or ask your users to click more slowly on your GUI... :-)
Yair