I am having the same issue. Did you find a solution for this For some users everything works fine, for others, the portal is visualized messed up. I found out why this difference is: if somebody deletes its cookies and browser history, it starts to get messed up.
We experienced the problem after detaching and re-attaching a content database. Or after publishing our portal through an ISA server. Both things happened between the time everything worked fine and when stuff got messed up. You got the problems too after one of both changes