I found a switch 'MINGW_IN_SHELL' that I use in my enivronment. Qmake will use this to apply the unix equivalents. Also, for anyone interested. Here is how I set up Qt, in my environment:
I set up a tool that runs this batch file
cd C:\Dev\projectname
set QTDIR=C:\Dev\Qt\qt-win-opensource-src-4.2.0
set QMAKESPEC=C:\Dev\Qt\qt-win-opensource-src-4.2.0\mkspecs\win32-g++
set MINGW_IN_SHELL=1
C:\Dev\Qt\qt-win-opensource-src-4.2.0\bin\qmake -project "CONFIG += qt thread" "TARGET = projectname" "DESTDIR = bin/debug" "DEPENDPATH = inc src" "INCLUDEPATH = inc" "MOC_DIR = moc" "OBJECTS_DIR = obj" "UI_DIR = ui" "RESOURCES = app.qrc" "QMAKE_LEX = flex"
C:\Dev\Qt\qt-win-opensource-src-4.2.0\bin\qmake -makefile
I run this each time I add a class or header. Then I set external Makefile under Project.