You need to know your boil off rate and have it entered correctly. You also need to know the loss to trub and the amount of top up water into the fermentor. All of that is in the equipment profile and you need to set it specifically for your equipment.
I just looked at the equipment profile for "Pot and Cooler (5 gal/19 L) - All Grain" in BeerSmith. It's default settings are showing exactly the numbers you posted above for pre and post boil volumes. If that is the profile you are using, then you need to modify it to fit your situation. Modify everything on that tab to fit your equipment.
+1
Once I got my equipment settings dialed in, the numbers that BS calculates have been nearly dead on each time.
Make sure that everything that you adjust in the profile is done from the profile tab and not from within a recipe. When you make changes to the profile from within the recipe, it only changes for that one recipe (not any future recipes that you create with that profile). If you want to see how those changes affect an already existing recipe, you can make the changes a 2nd time from within the recipe. BS does this intentionally so that changes to a future recipe will not screw up the numbers on previous recipes.
ForestGrove, ignore the gravity side of the equation for now, first you need to get your volume settings in order. Then, once all of the volumes are correct, as you adjust your efficiency the gravity numbers will fall into place as well.
The videos on the BS site do a fairly good job of explaining how to make the adjustments, but here is how I went through the configuration:
You said that BS calculated your preboil volume as 6.53 gallons, and that is what you collected. So that tells me your mash/sparge settings are already correct for the profile that you are using.
BS also calculated your post boil volume as 5.98 gallons and you actually only collected 5.
The .55 gallons that BS calculated as loss went somewhere, as did the additional .98 gallons that you did not collect. the lost wort is one of three places: cooling loss, boil off, or losses to trub. It is those three items that you will need to adjust in the profile to make the software match the real world.
I would leave the cooling loss at the default 4% as it is accurate enough for our purposes.
Most likely, your boil off number is incorrect. To calculate your boil off you will simply need to measure the volume of liquid before you start boiling and after the boil has finished (but before you transfer it to the fermenter). Subtract the ending volume from the starting volume and enter it into BS along with the amount of time you boiled the liquid. It will probably be somewhere around a gallon for a 60 minute boil.
After cooling the wort, measure the volume again, then transfer to the fermenter. The difference between what you started with before the transfer, and what is actually in the bucket after any straining that you do, would be the "loss to trub" entry in BS.
Once you get the volume numbers to match the real world, BS does a good job of calculating the numbers in the future. None of it is rocket science, it is really just simple math, but BS does make the calculations easier when you decide to do something like a 6 gallon batch instead of 5 gallons, or a 75 minute boil instead of a 60 minute one.
Hope this helped.
Kurt