I have the same type of thing. The gamma in windowed mode for my system seems to apply to whole system. Every application. If I click out of the window, like on the desktop but leave the window open, not minimized, the gamma fixes it self until I switch back into the window. If I minimize the window the gamma will not reset to normal windows settings when i click on the desktop or run other programs. I use windowed mode not only to play but also to leave a shop running while doing such things as web browsing or watching movies. As long as I leave the window open, not minimized I can do these just find with no gamma change. If I minimize the gamma settings from l2 will be applied to all my other applications.
The calibaration program that comes with the Huey has an option to "update for room lighting" at regular intervals (it has a built in light sensor in the colorimeter). It'll reset the screen color/gamma back to its calibrated setting no matter what program is running, even L2. No more eye strain for me in bright areas.