Here is what looks to be happening from all of my reading on the subject this evening.
MLB and the Pirates both believe that the contract that Pedro Alvarez agreed to verbally is binding. The view of MLB is that Pedro Alvarez is under contract with the Pittsburgh Pirates, because of Pedro not honoring his contract and or not fully consummating it, the Pirates requested that he be placed on the restricted list. As far as MLB and the Commissioner are concerned, Alvarez is Pirate property and is eligible to be place on that list.
The MLBPA has filed a grievance agsint the Office of the Commissioner stating that the office was in breach of the most recent collective bargaining agreement, by allowing drafted players and teams negotiate past the established deadline for signing such players. This breach of the CBA, not necessarily the ABC Affair, has caused this action by the MLBPA.
The Pirates, on their own accord, have said that the stalling of Boras and Alvarez are nothing more than a ploy to try to renegotiate his contract. Frank Coonelly lays out his side of the story in stating tha Boras made talks difficult and that he has not leg to stand on with regards to Alvarez, as his other high profile client, Eric Hosmer, was according to MLB signed after Alvarez. So if Boras says that Alvarez was signed after the deadline, then would not Eric Hosmer be as well. (As far as KC goes, Hosmer had stopped by in Kansas City, Dayton Moore sees no problem with his contract, and Hosmer has played in the minors already.)
Boras counters all of the allegations made by Frank Coonelly by saying the Pirates have not been straightforward and should come clean to their fans.
So what is going on here? Well the large picture is that the Pirates and Boras are caught up in the very storied rivalry between the Players' Association and Ownership. It seems that both entities have different readings of what the deadline means. The MLBPA sees it as a hard and fast midnight deadline. MLB sees it differently. According to this statement, by Pat Courtney, quoted by Dejan in his blog, the league extended the deadline for the clubs to negotiate minor league contracts, which are appearantly not covered by the CBA. Baseball America is reporting that the deadline was extended for the Royals and rumored to be extended for the Nationals and Pirates. If this is true it may take awhile for lawyers on both sides to fight this fight.
The other parts involve Boras and the Pirates. First if Boras were to make a stand in anyway against the draft system as it currently stands, the Pirates were the perfect opportunity. One the Pirates are run by Frank Coonelly, so a fight with the Pirates is essentially a proxy fight with the Commissioner's Office. Add to that the fact that Alvarez is viewed by many as the prime chip from this past draft, it was a perfect storm for a protest.
Boras is more than likely hoping to just wreck the draft process, whether it be any slotting stuff, the deadlines, whatever, he seems to be trying to hit the reset button with this move. He stands to gain a lot if things change, not so much if he gets to renegotiate the Alvarez contract (more money for Boras), but in the future if people start to really rethink the draft. Or he could be angling for more money by saying that Alvarez ok'd the deal himself without representation, a ploy that he tried over a decade plus ago with Alex Rodriguez. The ruling in that situation went against Boras, maybe he is hoping for something different this time.
The Pirates too are trying to do a lot as well. For one they want to save face. This franchise has enough bad PR, this is just heaping it on now. They also really feel that the contract is valid and don't want to pay more or even want to lose a player of his caliber. So there are selfish motives there as well.
But in looking at it, I feel that this is a part of a much larger conflict between players and owners. Boras has just taken the opportunity to try to give himself leverage and options. I like to think that the Pirates are acting in good faith in all of this, but sometimes that gets you left behind. There are a lot of very smart guys who will be debating this and trying to figure it all out, I can only hope that the Pirates end up on the winning end for once.