Whenever I go into fullscreen mode with F11 or the setting the colours from my Nvidia Configurations reset, my friend happens to have the samen problem. When you slide one setting from the Nvidia colour settings it direclty changes all settings back, strange bug, hope you can fix it!
Environment
Java 7 (last update), Windows 7 64 bit, MSI GTX 760
Perhaps for some reason the F11 button is bound as a hotkey for the default colour profile?