The roughness is most likely the result off unbonded metallic powders. Not having the flake thoroughly mixed will result in drowning (heavy flake in one area, minimal flake in others). Scottrods is correct about the flake not laying flat. Spraying at a lower kv will help with that. You could shoot another coat of a normal clear to smooth things out.
This explains bonded powders:
http://www.powdercoatingonline.com/h...d_Powders.html