During the course of a few pulls the naphtha began fogging up which is a good thing, however letting it sit and evaporate more is somehow making it LESS cloudy than before, which is really strange.

Has this happened to anyone or does anyone know why?

Potentially, the naptha was warm. Or hot. So when you transfered it to the evap dish the cooler temperature caused some crystals to reveal themselves to you, in the form of clouds.

As your naptha got warm, those clouds disappeared, because the increase in temperature meant an increase in solubility, and the crystals redissolved.

That is, my best guess with the information given.

This does happen and has happened me plenty of times , What it is the naphtha is becoming more to room temperature , It will come cloudy again as the naps evaporates and the naps will become more saturated again ...

Blow on the solvent gently. The cloudiness goes away once it sits in the dish for a while but returns when you have airflow across the solvent.