kdev and smi-mark,
A few additional things that might help us reproduce the problem:
What version of NuGet are you using?
How are you upgrading the NuGet packages? (i.e. via UI or Package Manager Console)
I'm using NuGet 2.2.40116.9051 and in both UI and Console the .csproj files are updated properly.
One more question: If you uninstall the package, is the .csproj file updated properly? Or does the issue happen in this case too?
Edited by sbelini - 05-Apr-2013 at 9:34am