Nutlaw, if you're really interested, here's a zip file of views to get started (at your leisure, course):
http://www.sadleague.allsimbaseball.com/STwaivers.zip
You'll find a few screens from before and during Spring Training, which typify the kinds of confusing signals the engine is generating. When I remembered, I tried to position my mouse to key in on the player to notice (I probably didn't remember it often enough), but if you view them in numerical order you'll get the overall jist: The AI puts players on waivers - in some cases even when it is a minor league contract! How does that happen? - when it moves anyone off the 40-Man (which means off the Active Roster in its case). I found that I can, however, drag and drop my own players from the Active Roster to the AAA club without having to pass through waivers. My recollection, although I did not test it in this series, is that if I use the right-click menu to move the transaction through I will be prompted to put him on waivers.
In any event, check it out. Notice in the first or second screenshot that it is the very day of the draft and the AI already places players on waivers. It is an odd assembly of logic at best, IMHO. Honestly, I hope you are able to look at this and point out something obvious I, in my ignorance, am simply either making too hard or overlooking altogether.
If you want to examine the process independently after this review, I would recommend starting a league, make sure after you do so you clear all service times, set the page to the league's Transactions/Major Transaction News or Complete Log and simply watch it unfold day by day, right-clicking on a player that may catch your attention and Open Profile to check his contract status (which will sometimes be Minor League and sometimes Major), but in every case his options all still remain.
Nuff said for now. Check it out when and if you have the inclination. Thank you again for your interest in helping determine whether this is a problem (I believe it is) and to what extent. Who knows? Maybe it will shed some light on waivers altogether.