Full info please. ALWAYS give as much info as you can- otherwise nobody can do anything but guess about what's going on and how to help.
What clearcoat are you using, and how are you applying it?
From what you've said, I'm guessing that you're clearing with TS-13, spraying from the can? And that you're applying your
rather quickly (all at once, or at least all in one afternoon)?
It sounds like the clear is being applied too wet and heavily, and that it is dissolving the paint under it. When this happens, the paint softens/reliquifies and the metallic bits that had gone down nice and even move about in random ways- changing the appearance of the paint in random patches. You cannot spray lacquer clear in heavy, wet coats- especially not over metallics or decals. It must be applied in many light coats, with an our or two between coats. Otherwise it will dissolve whatever it is being sprayed over.