The story goes Makerbot got really big on Open Source Hardware, this attracted investors, the investors demanded that the company lock everything down and some founders quit http://josefprusa.cz/open-hardware-meaning/
Yeah, the guy who founded them and wrote that blogpost, Bre Pettis, had previously publicly humiliated newbies to the community for not correctly releasing their hardware designs (because they didn't understand how), calling it "a dead end for the innovation and development which is the heart of the open source hardware community".
Basically, they're very keen on other people releasing their stuff as open source hardware so they can use it, but refuse to release their own stuff. It also doesn't help that certain prominent, business-owning members of the community called anyone holding Bre Pettis to the standards he expected of others terrorists and claimed to be standing up for "polite discourse" by doing so.
Makerbot disputes that investors caused them to change but "For the Replicator 2, we will not share the way the physical machine is designed or our GUI" http://www.makerbot.com/blog/2012/09/24/lets-try-that-again/