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Recently the OW was changed so that its caret would blink. This is fine, but the blinking should be turned off when the window loses focus. (Perhaps the caret should be hidden in such a case too, for full consistency with usual GUI text fields.)
http://hg.netbeans.org/core-main/rev/e54d55eeb9d5 or http://hg.netbeans.org/main/rev/e54d55eeb9d5