Alright, I didn't get enough time to play around with minor league totals and I have to crash, so I'm uploading this now.
CubbyFan's 2009 Release v3.0
Good news is DFA problem seems to be fixed. It seems that the computer just wants to run the DFA'd guys through waivers, and for some reason then does not remove them from waivers and cuts them when they pass through waivers.
This makes no sense to me and is probably some wacky AI, but I just removed them players from being DFAd and left them on the waiver wire, and the computer AI seems fine with that and won't try to DFA them anymore. I would recommend simming 3 days to pass all of those guys through waivers before you start doing anything as a manager.
Enjoy!
(also I always forget something, so please remember to allow ghost players on the league setup screen if you don't have a huge draft or auto fill the lower minors)