Check to see if your prefs are set so that command-tilde really switches windows.
Go to System Prefs -> Keybaord & Mouse -> Keyboard Shortcuts -> Rotate Windows
I had the same problem a while back until I noticed that an app added some service menu entries that used the same shortcut. I deleted the app because I wasn't using it anyway, but actually this goes to show that Apple should really give us more control over the services menu.
