I experienced same issue -- in my case narrowed it down to requireReinstallation="true" in my packages.config which had been (automatically?) inserted as a consequence of a retargeting to a newer framework. Removal of requireReinstallation="true" attribute returned build output windows to normal.
Ref. "Project Retargeting and Upgrade Build Errors/Warnings" in http://blog.nuget.org/20130814/nuget-2.7-release-candidate.html
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