Chris-
If you used a 'clear cote' of whatever as a primer, as you said, then I think you need to use another type of paint as a primer. A 'clear cote' will be too glossy, and hence too smooth for the purposes of being used as a primer. Anything placed over the top of it will 'slide around' and not adhere very well. If nothing else try using a 'flat' paint, like a gray, as a primer coat. Or try the auto primer I'm using.
My understanding of a primer coat is twofold. One is to give any subsequent coats of paint something to 'bite' on to, something to grab on to! The other purpose is to show off any flaws underneath. This gives you the chance to 'clean-up' that moulding seam you thought you cleaned up, but now the primer coat shows that you didn't quite do the right job, or that ejector pin mark you though you sanded down enough, and now the primer coat shows you it needs just a bit more sanding. Hope this helps!
Glenn