If you want to use 3D scatter plots you should click on tools/options/graphics/other graphic options.
Then click at the left of "use GDI for 3D graphs": check boxes are not shown but if you click on the right position the option will be activated.
HOWTO
Sometimes 3D graphs' windows will not close or minimize. If you want to
minimize them go to window/minimize all; then you can restore only the
worksheet and session window. If you want to forcibily close a 3D graph
go to window/clos all graphs. This however will close every graph in
Minitab.