[Zeke]

I think KT has nailed it pretty good, so I'll not go on too much. Large pieces of flagstone are hard to set on a complete, solid bed. I have used regular brick mortar and made bullseye circles and wiggled the stone down to grade. There will be a few voids. I like to pour in a mixture of runny sanded grout or even fastset anchor cement around each stone and leave that low. Then the final grouting can go in. If you like, you can cut channels in the base mortar to let the runny grout flow under more to the center of each stone, but really that should be well taken care of with the base. What I'm trying to say is, I favor the center of the stone for the base mortar and backfill the edges with the runny stuff before grouting. The acrylic modified stuff KT mentions is really good for the finish mortar, but hard to clean off the stones. Lots of masons don't like to use it on unglazed material.

Your other point about the pin holes being a result of entrapped air sounds about right. And, maybe a little too thin. They could mix it slower and let it sit for a bit before using. Probably have to be re tempered, which is not so bad of an idea.

BTW, what are the weather conditions? Have anymore questions, come on back.