Change fees have always been payable in "new dollars." The logic distinguishes between what you pay as a fare and what you pay as a fee. Once you give CO your $ for a nonrefundable fare it is usable only to pay a fare, not a fee. When you change itineraries on a nonrefundable fare you are not entitled to a refund in cash but may keep the difference in fare for application against a future fare (within ticket validity) and have to pay the fee out of pocket.

As to the other snafu - to err is human, to really screw up requires a computer. I wonder if the online change looked for a fare in the same class as you has originally purchased while a new searched found an available lower fare class?