test.exe
imaging-system.dll
imaging-system_mil9.dll
imaging-system_mil10.dll
Matrox.MatroxImagingLibrary.dll (the one from MIL 9)
Matrox.MatroxImagingLibrary.dll (the one from MIL 10)

imaging-system_mil10.dll
Matrox.MatroxImagingLibrary10.dll

test.exe
imaging-system.dll
imaging-system_mil9.dll
imaging-system_mil10.dll
missing: Matrox.MatroxImagingLibrary9.dll, Matrox.MatroxImagingLibrary10.dll

test.exe
dlltestDLL9.DLL
dlltestDLL10.DLL
mil9-x64mil.netMatrox.MatroxImagingLibrary.dll
mil10-x64mil.netMatrox.MatroxImagingLibrary.dll

private static void Main ()
{
  Mil10 ();  // when stepping into this, dlltestDLL10.dll is loaded
  Mil9 ();   // when stepping into this, dlltestDLL9.dll is loaded
}

private static void Mil10 ()  // when arriving here, dlltestDLL10.dll has been loaded
{
  testDLL10.CDLL10.Work ();   // when stepping into this, mil10-x64Mil.netMatrox.MatroxImagingLibrary.dll is loaded
}

private static void Mil9 ()  // when arriving here, dlltestDLL10.dll has been loaded
{
  testDLL9.CDLL9.Work ();   // when stepping into this, MissingMethodException is thrown, which is correct, because the EXE uses the already loaded DLL, which is the wrong one.
}

<?xml version="1.0" encoding="utf-8"?>
<configuration>
  <startup>
    <supportedRuntime version="v4.0" sku=".NETFramework,Version=v4.6" />
  </startup>
  <runtime>
    <assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1">
      <probing privatePath="dll" />

      <dependentAssembly>
        <assemblyIdentity name="Matrox.MatroxImagingLibrary"
                          publicKeyToken="5a83d419d44a9d98"
                          culture="neutral" />
        <codeBase version="9.2.1109.1" href="mil9-x64Mil.netMatrox.MatroxImagingLibrary.dll" />
      </dependentAssembly>

      <dependentAssembly>
        <assemblyIdentity name="Matrox.MatroxImagingLibrary"
                          publicKeyToken="5a83d419d44a9d98"
                          culture="neutral" />
        <codeBase version="10.30.595.0" href="mil10-x64Mil.netMatrox.MatroxImagingLibrary.dll" />
      </dependentAssembly>
    </assemblyBinding>
  </runtime>
</configuration>