^C is the official way. I sometimes see the symptoms you describe when there's a crash in a pyTivo thread (but the overall program keeps running). Normally that shouldn't happen.
Edit: There's also a "Shutdown pyTivo" button under the Settings page of the web interface, if you run under Python 2.6 or 2.7. I doubt you'd see different behavior with the crashed threads.
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Last edited by wmcbrine : 10-14-2014 at 03:25 AM.