I have recently stepped into the issue while rebuilding an existing project which I have checked out. NuGet correctly downloads the packages from its repositories on my hard-drive but VS seems not to see them in all projects in the solution.
I have reported this bug on Microsoft Connect page and will investigate this issue further.
What is interesting:
1. Libraries are on the disk.
2. In one of the project (this solution has only 3) referenced library works fine, and VS sees it.
3. When Uninstalled and then Installed (Re-Installed?) – everything is fine.
4. I tried changing “maximum number of parallel builds” to 1 – as it was suggested in a different bug which seemed to be the same issue (dependent projects etc.) – but this does not work neither.