right off the top of my head, I would suspect that either your grain absorption or mash tun dead space is off and that your boil evaporation rate is also off, compensating for the first issue. From the numbers you have (which is only partial information, so take this carefully and look at it in comparison with your other volume recordings), you have a pre-boil gravity of 1.051 or 51 gravity points at 16.4 gallons (I am assuming that this is at mash/mash-out temperature). Correcting for a thermal expansion of 2.6% at 160 F, actual volume at room temperature is about 16.4/1.026 = 16.0 gallons. Your pre-boil sugar points is then 16.0 * 51 = 816 points of sugar. Post boil gravity of 1.059 (59 gravity points) at 13.4 gallons (I am assuming at room temperature) is 790.6 gravity points. this is close enough at first glance to assume that the measurements are correct. So your boil off should be the difference of 16.0 - 13.4 = 2.6 gallons over 90 minutes. Your evaporation rate should be set for close to 1.73 gallons/hour. Check this number versus what you have in your equipment profile.

For diagnosing the pre-boil volume, you need to have a good measure of the amount of water used for both mash and sparge as well as what the actual volume of the dead space in your mash tun. If you do BIAB, the process becomes easier, as all the loss is to grain absorption and you can calculate this number by looking at the difference in volume in vs. volume out divided by the weight of grain you put into the mash. Otherwise, you will need to check the actual dead space volume versus the number in your equipment profile and correct that if it is different. Next, back out the dead space volume to perform the calculation for grain absorption and correct that in your global settings ('options' > 'advanced' > 'grain absorption'