Well, I suppose you see the mixed setup yourself!? I.e., you have two lines with QMAKE_MKSPECS, the second one wins. You have to recreate qt.conf in Qt's bin directory (which the old Setup-Qt.bat did) so that qmake finds it before the one it's actually loading - or find and edit this one to fit your setup.

A mind is like a parachute. It doesn't work unless it's open. [Frank Zappa]