I Had Unity 4.0.x, then tried to update to 4.1.x, suddenly MonoDevelop stopped working. It just doesn’t open and brings a very weird window error.
Then I reverted back to Unity 4.0.0, eventually updated to Unity 4.0.1, all without issues… Now Unity 4.2 was released and I finally decided to try and update. Same issue.
At the very bottom of Unity 4.2 release notes:
MonoDevelop may fail to start correctly on Windows if an old version of Gtk# is installed on the system. Please uninstall this version, and install a newer one if still needed.