The additional costs can come if the machine finds the tire is out of round. The system will then have the operator take the tire off the wheel and rotate it about the wheel to be re-mounted in a different position. If both the wheel and the tire have any raised spots you don't want them to be constructive making the whole assembly worse.
Obviously I don't know if this is why you were charged $100, but this can cause additional labour when balancing and could cause a variable price for the balancing.
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