Hi,
Calculating partial mash efficiency is notoriously difficult because the mash is usually a very small portion of the overall malt bill, and small variances in volumes and extracts can throw your numbers off quite a bit. To get a more accurate idea, try creating a separate mini recipe with just the mash portion of your recipe and using the brewhouse efficiency button to calculate OG and efficiency into the boiler for the amount of water you mash. This will give you an idea of where you are with mash efficiency, though your brewhouse efficiency will be lower than that.
Note that the estimated pre-boil gravity includes your extracts, so the 1.060 would be after you add your extracts.
Cheers,
Brad