Check the solderability of that component. An x-ray at the pin hole location will reveal more (ie how deep is the hole and how big internally).

My gut reaction is this is either some form of contamination of the contact pads or moisture. Examine the pads under a microscope and see if you can detect a contaminant.

Try a simple scrub with a pencil eraser and see if you still get the pin holes on that component. I would also try heating the board and component for an hour at say 120deg c to drive off any moisture. Add paste to the board and try a reflow.

Have you tried different reflow profiles? Have you tried a paste with a more active flux?

Without knowing the chemistry, it's hard to be certain. However, pinholes are caused by outgassing of volatile materials. These are caused by low boiling components in the potting/casting compositions, or are generated by the chemistry of these recipes while they are curing.

Some curing reactions will "give off" low boiling by-products, while other chemistry types do not. If I had more information, we could nail it down. Also, with proper equipment this could be absolutely proven (for example trace analysis of the vapors while curing occurs).

More info about the process and materials = MUCH better answer.