[ndcube]

Do you think that maybe the hop bag that I was using could be the culprit? I let it drain out before I took it out of the kettle, but I wonder if that is contributing to some gravity loss.

How many gallons are you making?  How much hops?  Leaf hops?

[Thirsty_Monk]

With regards to PH, wouldn't my preboil gravity not be good either if that was a problem?

Yes. Proper pH is important for good conversion.
But once your conversion is done in Mash tun you will not get less sugar in solution.

Could it be just some error in calculations?
I measure ONLY Brew House efficiency and do not botther with Mash Tun Efficiency.