I am having the same problem. Just to be sure, Is the Spritze database supposed to work the same way as the default where if you have "Automatically Import Historical Rookies" checked and the Amateur Draft is enabled, the Rookies should be imported directly into the draft pool? If the answer to that is no, the the rest of this post is moot.
I am starting in 1871. I selected neutralized stats and I made sure the Spritze database was selected. It imported 268 players for the initial draft. Then towards the end of the year when it went to create the 1871 Amateur Draft pool, it created and loaded fictional players instead. It then imported the 1872 Historical debuts on the first day of the off-season in 1872 (For reference, Jim Britt was one of these imports). When the 1872 draft pool was announced, only one Fictional player was created and the Historical Free Agents were not a part of it.
To be sure I didn't have any of the settings wrong, I also tested using the default files and the historical rookies imported into the 1871 First-Year draft like they were supposed to.
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