...and in that one post also lies the answer to the question
The flashing color is theme specific. It hasn't got anything to do with the window that makes it flash.
It might be possible to change the color on a per-window basis by directly patching the memory of your system, but I have never done that so I don't know how to do it (if it's possible in the first place).
If anyone manages to do it in any way, I'll certainly use it because I like the idea
/ 
