Man, that's always an issue...

First, you say its 100% the same paint? Same tint, same finish, same brand etc? Even so, its not unusual for the place that mixed the paint to get it wrong, or be off.. Its possible that dust and stuff flying out the vent discolored the area, but I would doubt it discolored the entire ceiling - just the path of air.. Does anyone in the house smoke? Did anyone burn the snot out of a dinner that smoked up the house? Did Cheech and Chong come visit?

The only things I can suggest are:
Painting the whole ceiling again
Getting a sample of the existing ceiling paint and getting a new can of paint mixed.. if its a small area, you might be able to get a sample can or a quart, at most
Maybe feathering out the touch up with a roller.. I've done that before - you barely load the roller with paint and let it run out of paint as you get further from the center of the touch up.. kind of feathers it out.. its a gamble, but if you hafta repaint the whole thing anyway, might be worth a shot..

You said you replaced the fixture, so I assume the new one is smaller, which shows the paint disparity.. You can buy - I dunno what they're called - beauty rings that go under the new fixture and hide stuff like you're dealing with.. Here's a link to somethin gsort of like I'm talking about..
[www.amazon.com]

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Friendship is like peeing your pants.. Everybody can see it, but only you can feel the warmth..