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At least on Ubuntu 8.10, a second popup window pops under the first popup window. The first time a second window pops up, it pops over the other; after that it always pops up under the first.
Could you please describe how I can reproduce this?
Sure. Select 'New'. The dialog where you can choose either a directory set, a file set or a version control repository comes up. Choose one. Now choose a file or directory using the browse buttons. The file chooser is shown. Cancel it. Choose a file or directory again. The file chooser will be underneath the other dialog.
R535: Fixed in svn