I assume you're talking about not reaching your expected OG. Just some things to check/think about:
First, what efficiency are you using to calculate your grain bill? I have my efficiency set to 75% in Beersmith and routinely come in around 4 points higher than expected. So I'm going to raise my efficiency to 80% and see if that fine tunes it a bit. If you have your efficiency set to 90%, and are only getting 75%, then that could explain it. Essentially, you wouldn't be using enough grain to achieve your desired gravity. Are you using roughly 10 lbs to achieve a 1.050 beer?
Second, check your crush. When I narrowed the gap to .025" to achieve a finer crush, my efficiency suffered (i.e. came in at a lower-than-expected OG). When I widened it again to .03" it returned to "normal. " I theorize that the finer crush slowed the recirculation and sparge enough to not extract as many sugars.
Third, check your mash time vs. temps. Are you getting full conversion? I know this is debatable, but if I'm mashing at 147 for a dryer beer, I usually let it go 90 mins. Conversely, if im mashing at 156 for a fuller body, it could be finished in 30 mins. Regardless, if I mash out too early, efficiency will suffer.
Keep on keeping on. You'll get it dialed in. Worse case if you don't want to go through the hassle of figuring it out: just add 1-2 lbs more of grain to your recipes and call it a day.