Oh no, I'm sorry you've run into this. When I was writing the new DC Motor tutorial the other day I noticed that this may not work as well as I originally though, but then I forgot to let you know about it.
The issue is the bridge control truth table for the driver IC (which is a DRV8848, by the way). The table is:
IN1 IN2 OUT1 OUT2
0 0 Z Z
0 1 L H
1 0 H L
1 1 L L
As you can see (and already guessed) it's not possible to drive both outputs in the same pair to the high voltage level. In addition, to drive them both to gnd you must set both inputs high rather than low, since setting them both low actually makes them high impedance.
If you want to get +5V out of the + screw terminal, you could connect all three pins of the power supply selection jumper. That would effectively provide +5V to both the driver and the + screw terminal. Just be sure not to forget about it if you ever hook up a higher voltage power supply.
I'm very sorry that I lead you down the wrong path with this. Let me know if this doesn't work out and I'll do what I can to make it right.