I still think it is great you did the help tooltip. I did some usability testing of the login screen and the WYSIWYG editor's file api integration, and it seems some users assume there is a tooltip when you hover over the icon (they did not use the popup at all so I do not know if they expected that).
One thing I realized though after having used the feature for a longer while myself: the implementation is not 100% in accordance with standard tooltips, after all. As you hover over question mark items accidentally, hitting them causes the tooltip with the animation to instantly appear, and this can be distracting. To me the effect is that I stop and wonder if there was something that I should have seen, I pull the mouse back towards the icon until I realize that oh, it was just the tooltip since I accidentally went over the question mark icon.
- Just like now, start loading the tooltip contents instantly when the user hovers over the icon
- Only show the tooltip, regardless of whether the contents have been loaded or not, after one second (one second delay seems to be the default in Vista http://www.google.fi/search?q=hover+delay+of+second&btnG=Search ; that is all I found quickly)
This should remove the distraction while not slowing down users too much. The delay is expected behavior and thus it does not impede finding the help.