Please see bug here for details http://nuget.codeplex.com/workitem/2970
As part of the fix it's planned to revert back change that was done with this issue http://nuget.codeplex.com/workitem/2608
<ResolveReferencesDependsOn Condition="$(RestorePackages) == 'true'"> RestorePackages;
would be replaced with
<BuildDependsOn Condition="$( RestorePackages) == 'true'">
in nuget.targets file
This would make package restore to happen when project is build instead of when assembly references are resolved which causes the issue.
Please update here if you have any concerns.