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Are you playing an independent team, or an affiliate?
I know it sounds stupid to recommend reading a 520 page manual, but somewhere in there you'll find instructions on how to set the AI not to mess with your lineups.
If I recall, it's a two part procedure, but I believe you start on the 'Manager Options' page. There are a series of options there allowing you to set either yourself, the AI manager or the bench coach to control various things like lineups, depth charts, promotions and demotions, trades and so forth.
After that you stop by the 'Options and Ballpark' page for your team (and probably your affiliate teams, if you have any). There should be a checkbox that says something like 'Prevent AI Roster Moves'. You may need to be in commissioner mode for some of these options to appear.
I'm not as familiar with 2007 as I am with 2006, so take what I say with a grain of salt, and don't get frustrated. Hopefully there will be someone along shortly with more up-to-date information.
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