Hi,
You can't do this with AppStylist, since there is no way for AppStylist to distinguish individual nodes in the tree.
In fact, I am pretty sure that the CheckBoxes in the tree are drawing using the WIndows API, and I don't think you can specify specific colors for the inside of the checkbox - it just picks up the WIndows settings.
The only way I know of to do this would be to use a DrawFilter and draw directly to the UIElements yourself.