For anyone who doesn't know, or has an issue with vista not doing what it should, the repair is now done from a command prompt (run as an administrator) rather than in XP where it's done from the 'run' app.
Just type 'sfc /scannow'. A vista disc doesn't appear to be required either. There's more information on the Windows support website.
This has fixed the issue that I had with my second machine that wouldn't shut down properly so it's definitely worth a try if you're having problems.