Factors that lead to excessive HRs -
1. Managers who emphasize POWER over fielding - Chicks dig the long ball. So do mouth-breathing, chest-pounding neanderthals. "Hey, who cares if the guy has 40 errors... HE CAN HIT 50 HOMERS!"
2. Tankers - In HBD, there is no penalty for going 0-162. You'll still get $185M next year, except now you'll get the #1 draft pick and first waiver wire position. If you deliberately draft a player that won't sign, you'll get the top TWO picks after you tank another year. So, why not trot out some horrible LowA level pitching?
3. Managers who don't check their teams every day - Not as bad as tankers (who do it every day), but capable of periodically sending out a horde of 0(0) pitchers for a nice little 28-2 game where they give up 12 homers.
4. Modified "fatigue" strategy - Not as extreme as the SLB equivalent, but guys will send out crappy pitching against interleague rivals in order to give their "real" pitchers an extra three-days of rest, which is important because HBD has pitchers with 15/80 dur/sta ratings (and NO starting pitcher in MLB pitches only every 6th day).
5. Park Effects - Check out the HR totals for Colorado/Santa Fe players and the road teams that play there. Subtract them OUT of the computations. You'll probably see much more realistic home run figures.
6. It might be the engine, after all... - But without isolating these other variables, ADMIN is just flinging poo at the wall, trying to see what will stick.