pH certainly does correlate with efficiency, especially if the pH is too high. This can happen if your water has high residual alkalinity and your grain bill includes mostly pale malts. Have you brewed any dark beers, and if so, did they do a little better in terms of gravity? The 5.2 product is largely viewed as bogus, BTW, but let's not go there since it seems unrelated.
I am grasping at straws a bit, as you've been brewing for 10 years (!) and using the same water for a long time. So really the question goes back to you: What is different with your Mash & Boil process vs. the all-grain system you used before that? (Which I assume got you better efficiency?)
I would try a very simple, small batch (1-2.5 gallons) with the same exact crush and water, without the M&B, and see how you perform. Remove variables from the mix so you can rule things out.