No manual recalcing is needed. As Brad K says the players Recalc just before the off-season. You are confusing this, I think, with League Modifier calcs.
First, back to the players, the ratings of the players depend on the recalc window. It can be one-, three-, or five-year recalc and be affected by other things like if you double count the current year ratings.
If scouting is on, that is clouding the true ratings. If at 100%, it's the actual ratings. Ratings on the 1-100 scale show the greatest granularity whereas smaller scales (1 to 10, or 20-80 by 5's, etc) can create a greater fog (and intentionally so) due to rounding.
Back to league calcs, on League Settings, Stats & AI, right-hand side, Accuracy Settings, ensure "Use Auto-Calc of Modifiers (Recommended) is toggled ON. Again, with this done, no manual running of calcs is required. There is a reason it is recommended to be on. Trust it..
