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I have noticed that if you do something like add a library using Tools|Libraries and click the "Add JAR/Folder" button, the file/directory browsing window consumes all available CPU for several minutes. This happens with Java 6 Update 3. If I use Java 5 instead, it's OK. But, I have seen other strange behavior where some of the folders get blanked out. i.e. there will be folder nodes in the UI, but they are blank.
*** This issue has been marked as a duplicate of 109703 ***