I have found BS to be a pretty accurate tool once everything is dialed in . Everything that the software does in terms of calculations is determined by the numbers entered in the equipment profile so that is the first thing to look at. If you have actual numbers for things like losses and dead space volumes then be sure they entered in properly as well as actual boil off. Some of these values can be determined by simply running plain water through your set up.
Personally I have found it best to NOT check any boxes that tell BS to do the calculations for you like adjusting volumes or boil off rates as find them to screw everything up.
It is also important that as you enter ingredients you look at the default values as those in BS may differ from your actual ingredients and these can be changed using the ingredients tab, especially AA values in hops.
Once all these things are tweaked the software should do a pretty good job getting things right and the rest is up to you and the process. If you are consistently missing your OG then there could be issues with your crush, mash, pH, meeting the proper volumes, rate of boil off and volumes into primary.
BS will help you calculate both mash efficiency and total brewhouse efficiency to help you win down where in your process things are going astray.