I would recommend working to dial in your process (equipment profile) to reflect your actual results. It would appear as though your grain absorption, boil off rate and mash efficiency all need to be looked at. On your next brew, or if you have the measurements from your last brew, record your actual water volume in (both mash and sparge), your collected wort and wort gravity pre-boil, your post boil volume and gravity, and volume to fermentor, volume of trub left over. From these you can calculate the amout of grain absorption, boil off rate and actual volume losses in your process. Use these figures to reconfigure your equipment profile (the grain absorption is a universal variable and can be found in your 'options' >> 'advanced' settings).
Once this is done, check your actual mash efficiency versus the projected efficiency from BeerSmith (it will give you actual vs planned numbers on the mash page). Use this number to reconfigure the Brewhouse efficiency in your equipment profile, adjusting the brewhouse efficiency number to achieve your actual mash efficiency.
Do this for the next couple of brews until the program has the correct settings to reflect your actual results better.