This is a known issue where Brightness Control can shift you off of your custom ColorSync color profile for your monitor and show your screen with default color values while fading.
We have this fixed in the next update of Brightness Control, but right now that update is sitting disassembled on a dusty shelf waiting for some free time.
We do have an alpha build that works (as well as an alpha build should)... The build introduces Brightness Control as a menubar item along with several other new features like hotkeys and multiple display control. You are welcome to download it here:
http://www.splasm.com/special/brightness/Brightness%20Control%201.1a11.zipIt hasn't been tested on current configurations very thoroughly, so use at your own risk. I have it installed on my current Mac and its been working with no issue. Thanks for the questions!