Re: PPG loss in boil?
The pre and post boil gravities in terms of dilution and boil off are not lining up - and this is independent of any software package, so let's try to figure that out first. Basically, I think as you understand, if you boil 10 gallons of wort starting at 1.040 down to 5 gallons, the resulting gravity will be 1.080. We should be observing the same pattern in your measurements.
The dilution calculator, 2nd section, comes up with the following:
http://www.brewersfriend.com/dilution-a ... alculator/
Irish ale: Boil 56 qts @ 1.046 down to 46 qt = 1.056 expected resulting gravity
Porter: Boil 51.2 qts @ 1.048 down to 44 qt = 1.056 expected resulting gravity
You got 1.050 and 1.063 respectively, those are both off, and in different directions. That tells us something is amiss +/-0.007.
Other things to check:
Are the gravities and volumes given
both temperature corrected?
1.048 @ 82F is actually 1.050 on a hydrometer calibrated to 60F.
Are you using a sight gauge on your kettle? Boiling wort is about 4% higher in volume, so if you are comparing one volume at boiling, and one volume chilled, it isn't apples to apples.
Are you adding anything to the kettle like sugars or water (except hops) during the boil that would alter the boil off dilution ratio?
About raw sugars in the boil:
The batch stats logic expects that raw sugars are not present for the pre-boil gravity reading, but are included in the boil complete reading. This is not related to the boil off gravity change inconsistency we are seeing.
In addition, profile settings would not impact this, except your cooling shrinkage factor.