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Closing a refactoring window "Usages of FOO" takes a long time if the number of usages is high. During this time AWT thread is blocked. See the attachment for one thread dump taken during the closing of the window. However, this is just one snapshot which cannot tell what is being done in AWT during the whole action. You must do a more thorough analysis.
Created attachment 14876 [details] Thread dump
We still need to investigate what causes this.
This does not seem to occur anymore (I tried it with usages of jEdit and other usages in MDR codebase and I never experieced it)
I did not see it lately too.