I didn't remember that particular legal complication, so thanks for prompting me to look it up. It seems that his argument was that Bukkit couldn't be distributed because it contained Mojang's proprietary code, but the fact that it also contained some of his code meant that he was a copyright holder for the purposes of the DMCA.[0]
This seems like an edge case that wasn't anticipated by the DMCA, but I can see the argument that mixing GPL code with proprietary code is creating and distributing a derivative work, in violation of the GPL. Without proprietary code being present, though, I don't think a developer can DMCA takedown their own GPL software.
