I have customised an MSBuild project so that the default target is a new target named similarly to 'BuildWithExternalReference'. This new target calls two other targets; the first is a custom target called something like 'BuildExternalReference' which builds a DLL using an external tool. The DLL that is built is a reference for the main project, which is built using the normal 'Build' target. I have setup the Inputs and Outputs attributes for the 'BuildExternalReference' target so the Inputs reference the source files and the outputs reference the resulting DLL.
In both Visual Studio 2012 and Visual Studio 2010 the build works correctly the first time it is invoked. However, on subsequent builds if I change the external source files (referenced by the 'BuildExternalReference' target Inputs attribute) then Visual Studio 2012 simply reports 'Build: 0 succeeded, 0 failed, 1 up-to-date, 0 skipped'. Visual Studio 2010 continues to work perfectly. In addition, building from the command line with MSBuild.exe works perfectly.