Whenever you have the Messages pane (Find-in-files results) shown and then hide it, sometimes the File Explorer's list view gets the height stuck at what it was when the messages pane was still visible. See lower left-hand corner of the attached screenshot.
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Steps to reproduce:
1) Be using Windows 7
2) Dock File Explorer pane on the left, on the Project tab, in Tree view
3) View -> Messages to show the Messages pane
4) View -> Messages again to hide it
5) Get lucky, as it doesn't happen every time. But once it does, it sticks there until you exit Rapid PHP