My team just ran into this problem within our build environment. The issue was due to a difference in the <HintPath> element of the .csproj file.
Our common assembly had a correct relative path to the directory containing our reference assemblies. The dependent assembly had a path from a former directory structure. The solution successfully compiled on dev machines as the GAC resolved the dependent's reference to the correct version installed in C:\Program Files. The build environment had a legacy install of the assembly (even though it should have had none) that it fell back to and thus the error. Updating the <HintPath> in a text editor corrected the problem.