I'm pretty sure that Mamewah cannot just be "copied" over directly to another computer, it has to be installed to ensure the correct dll files etc.. are transfered.
I'd suggest getting the installer from the Mamewah website, installing that on your 2000 machine, then copying your appropriate config files across (make sure it is the same version of Mamewah, as the config files changed structure recently). Also ensure that your rom directory paths are the same on the 2000 machine so the config files point to the correct locations.