The numbers used in the calculations, with the exception of grain absorption (see note below), all come from your equipment profile. They are user inputs. The numbers in the volumes tab you posted lead to a correct estimated bottling volume, so the calculations are correct. Your problem is likely due to measurement error, excessive boil off, one or more incorrect entries in your equipment profile, or a combination of the three.
Factory volume markings on equipment are seldom accurate and should not be used unless you've verified them.
Boil vigor and surface are major factors affecting boil off. Boil vigor is especially hard to control when using propane or CNG as a heat source, so is always suspect. Larger kettle diameters will lead to increased boil off so, if you've changed kettles you need to update your equipment profile. Weather conditions can also affect boil off to a lesser degree.
With the exception of boil off, the volumes needed for an accurate equipment can be measured. Be sure to enter accurate measurements, and not estimate any of these volumes.
Note: The grain absorption rate is not a part of your equipment profile, but can be adjusted if found to be a contributing factor.
