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I recently updated Unity to the latest version and it came with MonoDevelop 4.0.1. When working with MonoDevelop and Unity, sometimes the MonoDevelop editor gets to a point where it won't go behind any other programs, and even when bringing up the help menu or other modal windows within MonoDevelop, they show up behind it, forcing me to close the program and restart it.
This was fixed long ago. Unfortunately Unity shipped a long out of date (8 months, 14 stable releases) version of MonoDevelop.
*** This bug has been marked as a duplicate of bug 10644 ***