You cannot browse the \Windows folder from Active Sync or Windows Mobile Device Center. This is by design. You have to copy what you want to another folder on your device or SD card and then move it to the \Windows folder using your device's folder browser (or another file manager like Total Commander).
I've never heard or seen File Explorer not be able to see the \Windows folder from the device. Do you mean File Explorer from your PC or do you mean you're running File Explorer from the device and it doesn't show it?
But its very very slow in enumerating the files in the windows folder...so i would recommend your technique