As Tom points out, there is something wrong with the numbers. Looking at the numbers a different way, if you start with 12.5 gallons of 1.050 and the program says you should end up with 1.062, that means the program thinks you are ending up with 10 gallons, not 11, so it seems that your yield volume is going into the predicted post-boil calculation, not the end boil number.
Also, to back up another of Tom's points, are you sure about your volume numbers? Assuming your wort was mixed up well enough, using just your numbers if you started out with 1.057 wort at 12.5 gallons and you ended up with 1.061 after the boil, then that means you should have ended up with about 11.7 gallons post-boil. When you say you end up with the amount your're supposed to, does that mean you've verified the 11 gallons, or are you verifying that you've drawn off the 10 gallons you need?
Don't get too hung up on brewing software calculations until you get a handle on your brewhouse efficiency because that is the overall fudge factor that gets applied to your calculations. Even if you figure out that number, you can't even begin to talk about differences of a handful of gravity points unless you are very careful to do everything the same way every time. Do you measure your pre-boil volume as it goes into the kettle (150F) and your post-boil just after boiling (200F) or after you've chilled it (60F), or if you do it different do you account for the volume change? There can be a 4-percent difference just with temperature. You mention that you usually nail your pre-boil gravity, but then you say that sometimes you get much better efficiency, so I would argue that you aren't nailing your number if it comes out different than what you expect. However, if you've figured out your house efficiency and you are consistent, you can roll the new gravity number through BeerSmith. Even the Big Boys blend their beers to make up for differences in batch gravity (and color, etc.).