It is not entirely unexpected that missile defense became a stumbling block at the U.S.-Russian new START negotiations. Russia, of course, wanted to somehow limit U.S. missile defense program from the very beginning, even though it agreed that the treaty will deal only with strategic offensive weapons at first - the April 1st, 2009 joint statement that stated the negotiations is quite clear about that:
The subject of the new agreement will be the reduction and limitation of strategic offensive arms
It is not uncommon for Russia, though, to strike an agreement and then come back and ask for more - there were a few attempts to insert missile defense into the discussion since then (e.g. here, here). The U.S. decision not to deploy a radar and interceptors in Czech Republic and Poland helped to calm the waters a bit and for some time it looked like that the momentum generated by that decision would help carry the negotiations through.
Well, it didn't quite work that way. It probably couldn't have anyway, especially if the United States hoped that cancelling the third site would solve all the problems. It was, of course, the issue Russia complained about the most, but these complains had nothing to do with the specific configuration of the missile defense system. In fact, I wrote at the time that
any changes of the system configuration that would try to address Russia’s concern in a narrowly defined technical way – e.g. changes in the deployment area or a move toward mobile or ship-based interceptors – are unlikely to change Russia’s position on missile defense in a substantial way.
Unfortunately, this is more or less what happened - after a period of relative calm opposition to U.S. missile defense is back. This time it appears to be focused on the plans to deploy elements of missile defense in Romania, but I would argue that the specifics are again immaterial. As far as I can tell, what happened was that Russia found out that it again has no leverage over missile defense decisions - not even a sort-of-legitimate reason to complain about deployment in Poland and Czech Republic. This situation proved a fertile ground for a new mistrust and for all kind of statements about hidden U.S. motives. (We should also keep in mind that no one in Moscow ruined their career by insisting that the U.S. missile defense is directed against Russia.)
I have been long arguing that the only way to solve the missile defense debacle is to give Russia some stake in the process, probably by engaging it in a discussion of ballistic missile threats and possible responses and moving toward cooperation. In theory, the U.S. administration seems to understand it - it found the right words for the joint summit statement back in July 2009 and was generally supportive of the idea of cooperation. But something didn't work in practice, so we are where we are today.
I am still a bit puzzled why settling on the final treaty language is taking that long. As far as I can tell, missile defense is the only really difficult issue and a solution has been already found - Russia will make a unilateral statement stating that it would reserve a right to withdraw from the treaty if deployment of U.S. missile defense jeopardized its supreme national interests. The United States is expected to issue a counterstatement, saying that such a strong reaction would be unwarranted. Something like this was done at the time the START treaty was signed. Admittedly, the situation then was a bit different - there was the ABM Treaty to refer to. This time the reference to the link between offense and defense is supposed to be included in the treaty, which could potentially make the unilateral statement quite a bit stronger. (This already made some U.S. senators nervous about letting Russia to make any statements - Kingston Reif has a good summary of the controversy.) So, I guess it might be difficult to come up with precise language. But it should not be taking months.
The most frustrating part of this controversy is that it is about nothing - missile defense will never be able to counter any kind of missile threat, let alone give Russia any reason to worry about "strategic balance" or things like that. What we see is that missile defense proved again that it is good at poisoning everything.