It's not the metadata generator, nor the uninstallation of TD. The problem is that you're not doing a proper shutdown of pyTivo -- which isn't your fault, really, because it's hard to even do it properly in Windows. A proper shutdown with pyTivo.py relies on the KeyboardInterrupt event (SIGINT in *nix), and sends out a message to clean up the shares. Without this, the dead shares will linger, although they should still disappear after a time.
I'm guessing you used the "Windows Installer". Yes? You might see improvement by ditching that, and set pyTivo up by following these instructions. This uses pyTivoService.py, which (unlike pyTivo.py) is actually designed to run as a service under Windows.
I'm guessing you used the "Windows Installer". Yes? You might see improvement by ditching that, and set pyTivo up by following these instructions. This uses pyTivoService.py, which (unlike pyTivo.py) is actually designed to run as a service under Windows.