Hi there Han,
I had the same issue yesterday with a skin that has the logout button on the right of the page. There is a quick theming tip you can apply, by setting the z-index to either the mendixToolbar or MxClient_toolbar class to a value above 999.
Alternatively you can pick up the latest Environment Badges from the Mendix and Beyond blog. At the bottom of the post you'll find the link under "Update May 22, 2013". I've added a width attribute. It will allow you to shrink the badge to a size that no longer covers your logout buttons. I've set mine to a 100px width.
You will also find various other ways of sourcing your badges that could possibly help you solve the problem.