From all of the posts suddenly overnight on these threads, I get the feeling that one of the online leagues ran into this issue recently. I think I'm going to step out of the way of this train before it hits me.
I will say though, from my experience waivers seem to work correctly most of the time. They seem to get messed up in regards to players who are placed on irrevocable waivers.
The two things that I have seen which are broken appear to be:
1) Some times a player who is placed on irrevocable waivers will get claimed by a team successfully but for some reason end up on their previous team once the waiver time has expired.
2) In some cases the game does not seem to follow proper waiver priority rules when awarding a player. This seems to at least be true at the start of the season (in the first month when priority should be based on the previous season).
Since I am obviously not a developer, I can't comment on whether or not this is going to be fixed in the next patch or when that patch will be. As an online league commissioner and member, I obviously get frustrated by this bug too.