using AssemblySearchPaths in csproj files
Can you change the value of the "AssemblySearchPaths" property within the Target "BeforeResolveReferences" and see if that solves your issue?
<Target Name="BeforeResolveReferences">
<CreateProperty
Value="..\Dependencies\VS2012TestAssemblies;$(AssemblySearchPaths)">
<Output TaskParameter="Value"
PropertyName="AssemblySearchPaths" />
</CreateProperty>
</Target>