If you happen to change paths on subsequent builds of Revit, don't rely on the uninstaller to remove the Revit.ini file. It won't.
Make sure that you script the replacement or simply delete or rename the existing revit.ini to ensure that your new configuration gets installed correctly.
Note: If you choose "skip content creation" the product will automatically set the default paths to the location of the client install or default to program files....
Hint: You can edit the Revit.ini found under the admin image to fix the paths. If you rename the existing revit.ini found on the users harddrive, then your changes will get copied to the client folder install path.