Kilz3 spot treatment causing my ceiling to look like a different sheen on spot treatment

What is a coat of primer/joint compound mix? Never heard of it before, probably why it's cracking.

then a couple coats of cheap flat paint I had left over from another project, then put two coats of flat good ceiling paint with the paint sprayer. Came back the next week and paint was cracking ( not sure how or why) so I scraped the cracking paint off and applied joint compound in those areas and sanded down. Waited a couple days and put a coat of kilz 3 on the whole ceiling, while I was at it I noticed a few stain spots in another area of the house so I treated the spots with kilz3 as well with a roller, waited 1.5-2 hours and sprayed another coat of good flat ceiling paint on the two rooms. The room that I did the spot treatment on looked glossy even after the paint dried. I sprayed a second coat on that area and waited about 30-45 minutes and it still looked glossy. I?m going back after the weekend to check on it.

I've seen this happen with other paints. Like one time I put up a bunch of one foot square color test spots. Not extreme bold colors either, most were similar to the final color and same type of paint. They showed sheen differences even after two coats. Not easily noticeable, but with the light at the right angle you could definitely see it.

You could try sanding those areas with a fine sandpaper before painting again. Rolling instead of spraying would probably be what I would do though. If the ceiling is large and you don't want to roll the whole thing, roll the area where the problem is and see if it goes away. You'd be putting another coat on there which would help and you might get away with just rolling those areas instead of the whole thing.