If there is one thing I've learned about the OOTP community, it's that there is a very low tolerance for HR stats that are out-of-whack. If OOTP was producing bad HR results for everyone, these boards would be lit up like Times Square.
So ... are the league totals for HRs in your game close to what they were IRL. They may be too far off in your first season (though there are ways to keep that from happening), and maybe even a bit off in your second season, but after that the totals should be very close. If they are not, that's a big clue. If the league totals for HRs are historically accurate, then you have to look at reasons why individual players may be hitting a lot more or a lot fewer HRs than they did IRL (and the discrepancy has to be LARGE to be meaningful). That means looking at the Editor for a player in question, to see what game is giving him for a Power rating, and how many HRs the game expects that player to hit in a normal season. And so forth.
You can also do similar investigations for other stats that seem to be way out of line.