Linux Mint 13 Mate
java version "1.7.0_11"
Java(TM) SE Runtime Environment (build 1.7.0_11-b21)
Java HotSpot(TM) Server VM (build 23.6-b04, mixed mode)
When pushing any of the change buttons on the new project form the save dialog opens behind the new project form and not above.
Cannot reproduce it.
Could you please check if that error also exist on other environments & infrastructure.
I've tested it on Windows 7. There it doesn't happen.