I just upgraded to 9.0.6.1661 from version 8. I'm experiencing the same issue on both Win7 and Vista machines. Mine isn't quite as bad as the video, but if I have PLSQL Developer maximized and have 2 windows open and switch between them, the title bar, menu bar, and buttons/tabs in the view table/test window all flash for 1-2 seconds. The UI is unresponsive during this time. I can reproduce it with any window type (sql, view table, etc.). The problem only happens if PLSQL Developer is maximized. If I unmaximize and resize it to fill the screen, no flashing occurs when switching windows. I can also reproduce it by changing the login (or logging off). I am on the console of both machines (not RDP'd).
Both machines are 64-bit Windows with plenty of memory free. One machine is using the 11g client, the other the 10g client (I can reproduce the issue without being connected to Oracle - just switching back and forth between two SQL windows).