See if this thread relates to you. If you've installed Optional update KB2955164 and are not using the latest version of WB's (8.05), you will have what you describe.
Hold Ctrl while logging on to bypass WB then either uninstall that update or update to the newest version of WB's available in your account page.
Reboot and see if that has fixed it.
P.S. You are better off just using each programs UI to apply skins. Theme Manager is flakier than Granny's biscuits. You'll never get consistent results using it. (or trying to)