Hi,
I have occasionally seen problems like that myself, the theme cache is managed by asp.net and it should be invalidated in mojoPortal if the theme.skin file or the web.config file is modified and generally it works correctly but every now and then I have definitely run into this sticky theme cache problem where it seems to be stuck. In those cases I've resorted to things like recycling the app pool or even restarting iis or rebooting to get past it, though I know those things are problematic in a production environment. One less disruptive solution for production is to copy the skin with a new name and then change to that skin.
The theme cache as mentioned is managed by asp.net outside of mojoPortal control. We pass in one cachedependency that points to the theme.skin file and one that points to the web.config file to asp.net and that should make it watch those files for changes and clear the cache if they change. When this problem occurs it seems as if asp.net for some reason does not notice the changes to the files or in some way lost the references or stopped watching them.
Again I rarely encounter this though I have encountered it. In a dev environment I'd try a reboot.
Hope that helps,
Joe