On Windows 64bit machines you have to set the compiler flags manually in each configuration.
You have to set additionally: /bigobj /MP
CMAKE_CXX_FLAGS:STRING= /DWIN32 /D_WINDOWS /W3 /Zm1000 /EHsc /GR /bigobj /MP
CMAKE_C_FLAGS:STRING= /DWIN32 /D_WINDOWS /W3 /Zm1000 /bigobj /MP
These flags are considered as environment and should be set in the environment, eg. with the CL variable. If they are absolutely required for MITK we could check that they are set.