I'm not sure why that would happen; there's no particular rhyme or reason for it to be on. The tuner will be an 'always on' connection, but typically, that's the only one that is always on.
If you don't mind losing your picture settings, you might try holding down the EXIT button on the remote for 12-15 seconds until you get a "RESET?" prompt - that may clear up the issue, but I'd have no way of knowing if that master reset will be a guaranteed fix.
I recently retired an old DVD player that connected to my LN46a630 via AV1. There is now nothing plugged into AV1 yet it still shows in the list of available inputs. I find that inconsistent because other inputs like HDMI go away when not plugged in. I can't find anything mention of how to remove a source from the input list. Am I stuck with it forever?