Weeds,
Are those things you describe as 'fish eyes' actually small bubbles. If the first coat is trying to flash off, or dry, and a second coat is applied on top of it, it will create tiny bubbles as the vapors migrate up through the fresh coat.
I think if the first coat is dry enough to sand, when you apply another coat the finish should be fine. On small items, you can run a propane torch over the finish and the bubbles will pop and level.
If these are actually fish eyes, which are usually a ...well, a thing that looks like a eye on a fish!!..maybe something has contaminated your gun. They make fish eye remover..'Smoothie', which eliminates this problem and lets the finish flow like glass. I don't know if it is compatible with your finish, but you might investigate. Good luck.
Stuart
