Glad to hear that, did you edit the menu with Menu Writer at any point? The default files have these values set as:
$WA_localRoot = "" .$WAGLOBAL_localRoot ."";
$WA_remoteRoot = "" .$WAGLOBAL_remoteRoot. "";
They should not be updated unless you make an edit with Menu Writer. Thanks for mentioning the CMS images, I'm sure this will be helpful to any others looking to do the same thing.