[BirdWatcher]

I can't speak to the 1880's portion of this scenario, but I did experience odd inflated homer totals in my fictional league in that save's 1981 season in the minor leagues.
It did appear that something had gone awry with the statistical modifiers for the minors but I went in and made sure that just prior to the start of the next season I went through each level of the minors and manually chose the 1982 statistical modifiers for every level and this season everything is back to normal, with the homer totals in the minors basically matching the major league statistical environment.

I don't know how much you can fix this for an ongoing season, but I would think that adjusting the modifiers for homers at each level of your minor league systems should start to get things back to normal.

EDIT: Sorry, I don't feel like that was very clear. Long work week, Friday night fuzziness, and watching the Tigers-Blue Jays game so probably a bit preoccupied. So to bottom line it: I feel your pain, it can be fixed.