There are two possibilities as causes for your glossy flats:
Incomplete mixing. This is the most common cause. If the pigment is not completely mixed in, or if the flatting pigment has clumped up with itself or some of the color pigment, then the binder forms a glossy surface. Try mixing (stirring) the paint for at least five minutes. If you have a powered stirrer, all the better. If that works, well and good.
Sometimes the flat pigment clumps together (the technical term is flocculation). You probably won't see the clumps, as they are only slightly larger than the original particles and still microscopic, but if this happens, there is no way to fix it.
Some drying conditions can also produce a similar effect, especially if the paint is laid on very thick. Try multiple, thin coats rather than trying to cover in one. A small amount of thinner may help in such situations.