I have been dealing with this issue from the beginning of ootp2007. I have the minor league managers deal with Minor League Transactions and Minor League Lineups/Depth/Pitching. I'll have young talent in the minors and the minor league manager will release them really early. For example, I had a catcher, drafted 5th overall (potential rating of 79) who was released less than a month after he was drafted.
I had the exact same setup with 2006 and the minor league manager would never cut good talent. With 2007 however, I've lost quite a few players when there seemed to be no good reason for their release.
I am running with the beta patch.
The folder is shared at
http://brabnet.4shared.com/
with a password of ootp2007 (use this to both access the site and the download)
Any help would be appreciated.