I have a problem while drawing with both GDI and GDI+ interchangeably. The page transformation—in particular scaling—seems to be a little bit off between the two. Wh
One thing to remember is that most of GDI usually runs on the hardware (i.e. GDI functions map to the display driver that implement some functionality on silicon) GDI+ was supposed to get hardware acceleration, but it remained as a software alone renderer.
Try manually setting a few pixels via GDI+ and GDI and see if they differ.
Perhaps the way your particular graphics card transforms co-ordinates deviates from the way it happens in GDI+