Difference in MSBuild and Visual Studio Build?

I'm working on a MSBuild script that will retrieve all the sources from TFS and build all the Solutions. To my surprise one of my MSBuild scripts raised errors on a solution that was building fine in Visual Studio. In MSBuild I got the following error: "The type or namespace name "name" does not exist in the namespace "namespace". (Are you missing an assembly reference?)".

After a long hard search I found a stray projectreference in a project file (*.csproj). Usually all the References and Projectreferences are packed together in one ItemGroup, but in this specific project file there was one ProjectReference in a seperate ItemGroup at the end of the file. This was exactly the project that contained the namespace "name". I copied the ProjectReference to the ItemGroup containing all the other References and deleted the stray ItemGroup. This fixed the MSBuild errors.