From my experience, the issue here is that as someone pointed out, there's no where "up" for the players on unaffiliated teams to go. A bigger problem, IMO, is that the minor league free agency setting doesn't seem to apply to players on unaffiliated teams.
You will also see the unaffiliated teams sign players to extensions--"major league" extensions, but not to the extremes as before--but those extensions never actually come into existence because free agency isn't working.
The only real work around is to manually go through unaffiliated teams and make sure the best players are "released" so major league organizations (or foreign leagues--or what have you) can sign them. Probably less of a bother for people who like to play in "God" mode anyway (like myself), but a huge hassle for others.
|