This is a little off topic, but I'm curious, why play with foreigner restrictions? When I first got X, I thought this might be fun, till I started playing it out. Then I realized trades, drafts, free agency, all that is out the window, because if they weren't my nationality, they couldn't be on my team (or if they were my nationality, they were mine anyhow). It seemed to just remove a lot of what I can do to manipulate my team.
(not trying to be critical, play your game your way
i'm just curious what you are accomplishing. Maybe I missed something, and you can re-instill this interest in me)
EDIT: After thinking about your problem tho, the problem is just with randomly created players during the inauguration year right? So just don't hit that button to fill the league with randomly created players. The minor league teams will only pick up players when they are given to them by the parent team. If the parent team is restricted to nationality, it can't give a minor league team a player of another nationality (i'm guessing here). So, don't inject the minor league system into your game, until you have a sufficient sized reserve on each team. Once the reserve is full (25+?) then create the minor league, and the AI will move players from the reserve into the minors, and fill with the proper nationality (still, just guessing).