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This happens under the "Files" tab (not the "Projects" tab). I'm pretty sure this didn't happen in Netbeans 5.5. You do not need to make a change for this to occur, just click Ok and it should collapse all open folders. This is with Netbeans 6 nightly build 200708201200
Reassigning to "core".
Not sure if you open project properties. There is missing step in your description because right click on project node only shows popup menu. I open Properties and press Ok and tree in Projects or Files tab stays unchanged ie. it stays expanded it si not collapsed.