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Playing with the default database, you will should not get that many available players for the draft unless import & maintain real minor leagues is checked. The downside of this is having your minor league team names and setup changed by the game, but it will give you the draft numbers you are expecting. That setting must not have carried over with your import for some reason.
For example, running 1985 Jays with a 26 team league, I had enough players for a little over 5 rounds. With the Import minors setting checked I had enough amateurs for 43 rounds.
This setting is initially set in the game creation screen on the first panel of the wizard under the selection for Import Complete History. If you go ahead and change it in your current game via the setting in the screenshot below you should see the larger number of players you are accustomed to the next time a pool is generated.
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