Because they're the ones with the power to give your license back, so you either do what they say or spend the next year without a license trying to work out what went wrong. They're the court - nothing happens to them when they screw up.
However I got a $285 ticket proving it yesterday. Courts aren't open on the weekends so my lawyer will be figuring it out tomorrow.
I will be in the DMV first thing in the morning to try to get a new license so I can travel home (went to parents house for Holiday). I have to pay a $65 reinstatement fee tomorrow to get a new license as well.
I assume the payment did not triggered the right things to mark the fine as payed, or someone made a mistake a number somewhere and something failed. You should always keep your receipt for a while or forever (keep energy/phone bills for a few months)
People aren't going to trust a receipt over the system they use. It's as simple as someone checking their computer seeing that OP never paid and then forwarding it to the right place. It's not like the cop has the power to override the system because that would be nightmare in terms of accountability and potential abuse.
Yea, it sucks and it's unfair, but there's nothing unbelievable about it. For any set of rules, there are always going to be people that fall through the cracks.
As an aside this is a good reminder to keep forever any receipts for settlements with courts, the IRS, or other regulators.