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This might be a problem for the JDT gang, but it seems to only be appearing in the GTK version. Open up a java workspace, and select a method (click once). Left click to bring up the context menu, go down to "References" and search in the workspace or hierarchy or whatever. If you have just opened the workspace, the program will beep. I guess signalling nothing found. If you double click on the method instead (not quite sure the difference, though I think double clicking causes the method's name to be selected in the editor pane). Then try finding the references again. It will find them. The real problem is after a reference has been found-- you usually click twice on it to bring it up in the editor to look at. Then if you go over to the overview pane again and either (a) click once to select and then right click on a method or (b) just right click on a method, you will instead find that when you search for references again, you will bring up the references that is highlighted in the editor. Quite confusing!
sorry, forgot to mention: release 20020125
Sounds like focus issues.
It's the "random focus grab". We have resolved some of the symptoms, but some weird things are still happening. Right now, this is marked "priority #1".
Fixed.