a year or so ago I had a problem with both of my tivos (1 series 3 and 1 premiere). some stations would not come in at all, others were supposed to be one station, but were broadcasting the wrong station (example 1026 in my area is pbs hd. when I tuned in to 1026, I got Univision hd).
eventually we determined it was an error that originated from the programming that messed up the internal tuning.
the only solution - we did work - was to clear and delete everything and start all over. that corrected the problem and all the stations were coming in correct after I did the clear and delete.
not sure if this is your problem, but thought I would let you know my experience, just in case.