I followed the link and found this:
When pressed as to why it’s taken over three months to get to this point, Selig said: “The clubs tried to settle it themselves and I had a lot of patience because everything controversial ends up on my desk. In this case, I did give the clubs more latitude, both Chicago and Boston, in the hope they could come to some conclusion but they didn’t and it’s OK, so now I have it.
“That’s the way baseball is set up. If the Cubs can’t solve their own dispute, then the commissioner does. After 20 years, I accept that as part of the job and I don’t really think too much about it.”
http://www.csnchicago.com/blog/cubs-talk/post/Selig-on-Theo-compensation?blockID=640006&feedID=619
my emphasis
Selig seems to be placing the onus on the Cubs - so who do they have? 
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