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"I thought they were a 527 as well, and they are actively campaigning for Obama. I am on their list and have been uncomfortable about them endorsing someone ever since they did so. Can someone clarify how/if this is different?"
You are correct, there is no difference. But it is up to the Clinton campaign to file a complaint against MoveOn. The Clinton campaign might be hesitant to do this because they may want MoveOn's help in the general election.