When you do Humanoid:MoveTo(pos, part), it goes to pos based on the part, which is defined in the Humanoid's WalkToPart property. WalkToPart actually never goes away if you were to do Humanoid:MoveTo(Humanoid.Torso.Position, nil) to clear that WalkToPart property. Because of this, if you had set the WalkToPart property and later wanted to go to another point via MoveTo, the WalkToPart property would remain there and would offset where the character goes.
How would I manually set the Humanoid's WalkToPart property to nil? I really can't think of any way except setting the second argument of MoveTo to nil, which doesn't seem to work. Maybe it's because back when you set the second argument of MoveTo to the part, that moveTo never finished? I am not sure and that shouldn't happen because of the 8 second timeout.