I have a css rule defining the background color as the window system color:
background-color: window;
When I try to get the background color using jQuery's css method: $(selector).css("background-color");. It works well in Google Chrome, it returns the correct color, albeit not as a system color, but translated to rgb(255,255,255). In IE9 it returns rgb(-1,-1,-1)... Which of course renders black and not white when applied.
May not be the "answer" you're looking for - but a couple of notes:
As to "why this happens" - see http://msdn.microsoft.com/en-us/library/ie/aa358804(v=vs.85).aspx - particularly:
Unlike the other named colors however, user-defined system colors have no numeric RGB equivalent because the exact color is not known until the Web page is viewed on the user's system.
also note:
The system color names have been deprecated in the Cascading Style Sheets, Level 3 (CSS3) recommendation.
If it is an absolute requirement that you be able to determine the RGB color code of the user's system-color for window on IE then you could resort to https://developers.google.com/chrome/chrome-frame/ to bridge the gap