You say your pre-boil measurement is adjusted for temperature. Does this mean you cool off the wort before measuring, or does it mean you measure hot wort, check its temperature, and use a correction for this?
I find that if I measure hot wort and calculate the "correct" SG using Beersmith or similar tools, the number I get is higher than when the wort has cooled off. In other words, if I measure hot pre-boil wort, I will overestimate my pre-boil SG. Could this be your issue?