Pre-Boil Gravity & Mash Efficiency

I have my brewhouse efficiency set at 65% and my equipment profile all set up correctly.
I did a partial mash recipe and overshot my OG by .001 giving me a brew house efficiency of 68%.

However, my question is about my mash efficiency. I seemed to hit my numbers fine at the end, but my pre-boil gravity reading seemed extremely off. It estimated a gravity of 1.108 @ 73.6% and I got a reading of 1.073 @ 12%.
I mashed with 8.25qts for 6lbs of grains and I batch sparged with 8qts split into two additions.
I use .5gallon of boiling water in the kettle as a mash out when I drain the mash tun. And then I topped off with another .5gallon in the kettle to reach a pre-boil volume of 3.75gallons.
When I get the kettle up to 200degrees I add only 25% of my LME (add the last 75% of extract with 15mins left in the boil) and then I drew a sample and dropped the temp to 70degrees before taking a gravity reading.This is when I got a reading of only 1.073.
Is this the wrong time to take a pre-boil gravity reading?

I'm not sure what I am doing wrong since I was able to surpass my overall brewhouse efficiency in the end.

It sounds like the software is expecting you to add the entire amount of extract at the beginning of the boil.  Try lowing the extract amount in your recipe and see if the numbers come close to matching.  As for the timing, you are right on for the time to pull the sample.  I would suggest you invest in a refractometer.  You can find good ones on ebay and they are pretty cheap.

I have my extract set as two separate additions with the 2nd addition having a "late extract boil time" of 15mins.
So you would assume that if it lets you set the extract this way that it would account for that in the pre-boil gravity



---Update---
I did a test and just deleted the 2nd extract addition that is set in the software as a "late addition" at the end of the boil and my pre-boil gravity dropped from 1.108 to 1.058.
So I'm guessing that the formula in the software that calculates the pre-boil gravity isn't taking that late addition into account for some reason, even though other measurements, such as the estimated IBUs, do take this into account in their formula.