I have a sight glass on my kettle that I calibrated when I built my system. It is pretty accurate. I have attached the .bsmx file here.

Like I said, I get consistent results by doing the calculations by hand, it is just a bit perplexing that I get numbers that are so far off from the software.

First glance, you have entered the preboil gravity in for your post mash gravity. I am guessing that your post mash gravity contains the contribution of the sugar addition. If you drop out the sugar addition, your post mash gravity would drop 17 points. This 17 points brings the post mash gravity reading to 1.051, which still gives you a mash efficiency of 96%.

The reason that the post mash gravity measurement is in the program is specifically to remove the impact of the sugar/extract additions made before the boil in order to correctly calculate the mash efficiency. Otherwise, this number would be influenced by the sugar contribution and give you an inflated value, which you are seeing in your recipe.

You will please forgive me for using metric units below, but I work in metric as it is so much easier for conversions:

The second issue is that your sugar point balance does not work out properly. You have 28.39 liters of wort at a gravity of 1.068 at the beginning of the boil. This gives you 68 points x 28.39 liters = 1930 sugar points. Following your boil, with the zero trub loss you have indicated in your equipment profile. You end up with 19.61 liters at a 1.087 gravity reading. 19.61 liters with the thermal expansion is 20.43 liters. Your ending sugar point total is 20.43 liters x 87 points = 1777 sugar points. With no other losses in the system, these numbers should be the same (or nearly the same as some depends upon how accurately you can measure the volumes). This makes me believe that there is one measurement which is not correct.

Another good reason for taking a post mash gravity reading, which with a refractometer is really easy, before the addition of the sugars is to help identify if there is a number which is inaccurate. If you have gotten a post mash gravity reading of 1.046 and then measured your pre-boil gravity at 1.068, I would think that you either over added the sugar or that one of these readings was in error. In fact, if you take your target gravity reading of 1.063 and volume of 28.39 liters, you end up with 1788 sugar points, which very nearly balances out and is probably within your standard error for volume measurement.

Edit: As an additional check, I looked at your boil off rate. You have 7.57 liters/hr in your equipment profile (2.0 gal/hr) and taking your volume measurements as actual you are getting 7.96 liters or 2.1 gallons for a 60 minute boil. This is pretty good confirmation that your equipment profile is pretty good for boil off rate. This points even more strongly to the pre-boil gravity measurement being off.