First, I'll assume you are a RHP.
What you are describing, if I'm understanding properly, is that your pivot foot remains in contact with the rubber through your delivery. If you go to the plate that way as part of your natural pitching motion, that would not be considered a balk.
The only thing I can think of, is that a pivot heel lift is often the first indication of a pick-off move and the umpire is not used to seeing this as part of a delivery, but the heel lift alone is not a pick off--especially if you are doing it into your lift when it would be clear that you are not attempting a pick-off. If you were a lefty, he wouldn't even be looking at your heel, so I don't know why he's looking at it for a righty.
What I would suggest, if you can't pitch without lifting this heel, is that when you first engage the rubber from the stretch, you do so with the heel up and don't let it contact the ground again. That would eliminate any ruling that your lift is deceptive.
In trying to simulate this heel lift move, I found that starting with my foot flat, I would lift that heel before my leg lift and I'm going to guess that you may think you do them together, but you actually precede your leg lift with this heel lift, which may be questionable.
Does this help?