You've got something in Carbonite's options messed up, that's why your set-up works the way it does. I changed my settings and took some screen shots.
It does work, just takes a little patience. You will notice the Blizzard minimap in the upper right corner of my screen.
Options.
Options
The options screen shots will show how the options are set up for this. I hope this helps you out in some small way.
/EDIT: If you go to the "Maps" sub-heading, then the "Minimap Button Options" tab, you can activate the "Minimap Button Window" in Carbonite's options. You can lock it in place,too, so it can't be moved accidentally.
You can also get an addon to put the minimap buttons in.
MinimapButtonFrame is a good one.
/END EDIT