Touch up paint not blending in

I worked for several years in a panel beating / Garage workshop, and first thing we did each morning was to turn on the stirrers in the paint room, and they would turn on and off throughout the day. This was especially important when a new tin was opened. And for any painting job, the stirrers would be turned on manually for twenty minutes or so before mixing a color prior to painting. I know that hand painting and spray painting are two different things, but the basics remain the same. If I was hand painting interiors or exterior of the house, I'd put a stirring paddle on the drill, and run it in the paint tin for a good few minutes. When it's done like this, it will have a better match.

I'd say you're right. Some of the darker colours are denser than the white base pigment and settle to the bottom and you get that effect at the top of the can when you leave it sitting up for a period.

A good stir and also try blend the brushstrokes into the surrounding area a bit better. Also when patching like this try brush in the direction of the main window or light-source in the room, that way you don't have the light falling across the ridges left by the brush-stroke and it all blends-in better.