However, I noticed that whenever a code window gets focus again (after selecting outside the code window), the color emphasis are ignored when refreshing the contents of the window. Could someone point me to the object with this responsibility ?.

Ernest -- Try changing the StandardSystemView of the window in question to a ColorSystemView. This version caches an image of the window at display depth rather than assuming that a depth-one image will do. The StandardSystemView is probably called out in an openOn: method. You will probably have to change several.

Another approach might be to define one or more "quick color" keys that add color to aid in some specific debugging task. You could then let the color revert to normal when you didn't need it. This would be kinda like clicking on a left parenthesis to find the matching right. Good luck. -- Ward