I've found that if I heat the jighead for too long on the hookeye, it will get filled with paint. Also the fluid bed helps with using a quick dip. About two out of ten hook eyes will still get filled though. Is there another way or technique I could use to ensure it never happens.

There are guys that hold the jig with forceps by the eyelet, this keeps the powder from filling. I personally don't do this. If I get a eye that fills, I immediately get a drill bit and shove it through the eyelet. This will clean it out immediately. Make sure you size the drill bit to fit the eyelet before you start painting.

I hold the jig head by the hook eye with needle nosed pliers.  I heat it, then dip it, then hang it and less than 1 out of a hundred get paint on the eye.

I heat holding jighead by eye with needle nose. Then hold with a cold pair for a few seconds

I just use a small diameter piece of wire and poke the the paint out of the hole if it gets any in it.