I ran into a similar problem. When I created a skin I found that certain elements would still show up as the default.css elements . If I understand correctly you ave to add portions of the default.css style to your skin.csss style then change the colors etc. The example below shows how to change the links on the pages. If you dont add the parts from My Skin.css to you custom skin css the links will remain the defaults blue. Im pretty sure that anything you want to change from a default has to be added and changed in you custom css file