I just tried to compile MITK tag v2016.11 on Windows 10 with Visual Studio 2015 in 64bits, using the official release of Qt 5.6.2, in Release and Debug. In Both cases I had to run the superbuild twice to obtain a full success.
During the configuration with cmake-gui (cmake version 3.7.2) I just added the path to Qt, the rest is default configuration.
Is there a known dependency problem between modules? Someone had the same problem?