I had a similar thing happen a while back when I was first trying to run a historical sim with full minors filled with fictionals. I can't remember the exact solution, but it boiled down to each league had its own draft enabled and each had 'use historical rookies' enabled. The minor league's drafts were bypassed for some reason and all the rookies were dumped into the free agent pool with a new copy made for every league. Seeing 5 Chief Benders on 5 different teams was my first clue.
So, I suggest looking at your draft options and how you import historical rookies. Sorry I can't be more specific as this happened some time ago.