QMAKE_CXX.COMPILER_MACROS is not defined error with QT 5.9

[oracle3001]

I have been using 5.8 for VS2015 64-bit on Windows 10 with no problems.

Today I have upgraded to 5.9 using the online installer, and changed the chosen version of QT in the QT VS Tools addon. However when I try and open a .pro file (which was previousy no issue) via the QT VS Tools addon, I get the following message.

--- (Import): Generating new project of libQGLViewer-2.6.4.pro file
--- (qmake) : Using: C:\QT\5.9\MSVC2015_64\bin\qmake
--- (qmake) : Working Directory: D:\sdks\x64\libQGLViewer-2.6.4-64bit
--- (qmake) : Arguments: -tp vc "libQGLViewer-2.6.4.pro" -recursive QMAKE_INCDIR_QT=$(QTDIR)\include QMAKE_LIBDIR=$(QTDIR)\lib QMAKE_MOC=$(QTDIR)\bin\moc.exe QMAKE_QMAKE=$(QTDIR)\bin\qmake.exe

--- (qmake) : Environment variable QMAKESPEC overwriting Qt version QMAKESPEC.
--- (qmake) : Qt version QMAKESPEC: C:\QT\5.9\MSVC2015_64\mkspecs\win32-msvc
--- (qmake) : Environment variable QMAKESPEC: c:\Qt\5.9\msvc2015_64\mkspecs\win32-msvc

**[1] - c:/Qt/5.9/msvc2015_64/mkspecs/features/toolchain.prf:129: Variable QMAKE_CXX.COMPILER_MACROS is not defined.
[2] - Project ERROR: msvc-version.conf loaded but QMAKE_MSC_VER isn't set**

--- (Import): Error(s): 2
--- (qmake) : Exit Code: 3

I have never had this issue before. The usual environment variables, QMAKESPEC and QTDIR, is setup as required.

Note:- One thing I noticed was when I installed Qt it set the QMAKESPEC to a non-existent directory, C:\QT\5.9\MSVC2015_64\mkspecs\win32-msvc2015, which interesting used to be the default for 5.8. Now all that exists is ...\mkspecs\win32-msvc.