Some IE box's seem to refresh properly and completely if you hold the Ctrl button down while refresh (<Ctrl><F5>).
Others, If I make the change below it will work (most of the time):
Press the Browsing history settings button to get the second window.
R_
If you are at 10.1 or later you have to overwrite your map service to see changes to layers, such as a color change, label change, or visibility or scale changes
I sometimes have to refresh the application in IIS Manager.