I'm using a modified version of zenburn, and I changed my lineHighlight to a darker color (my old eyes appreciate a little more contrast).
When the editor has focus, the color is exactly what I expect. When the editor doesn't have focus (like when I'm clicking on errors in the build results pane), the highlight line is not the color I chose and is a washed out version of it.
I went looking for a definitive list of colors thinking that maybe there's a version of the setting for the editor when it doesn't have focus but couldn't find any.
BTW, love Sublime 2, bought it the first day I used it and now use it on all my systems. Great Job!