I'm sure your other drivers will be usable, but they'll need a bit of fixing in the code, and of course the one you linked to is only one axis - I guess you have a pair of them.
Did you have any success running the standard adafruit motorshield code examples?
I haven't ever piggy-backed the L293Ds, but then I only ever run at 6v anyway, so I can get away with a little heatsink. Whether you are putting the power in through the arduino or through the external motorshield terminal, as long as the jumper is on, then the L293Ds should be getting the full 12v. If the jumper is off, then the 12v must enter throught the motorshield power terminal.
I'm not sure what you mean when you say the pen test completes, but with only one motor running? Does it just draw a straight line then? Is the other motor loose, or locked?
When you lock the motors (with a "set home", for example), are they solid? Can they be moved by hand? Also, when moving (assuming they can do it), can the movement be stopped or diverted by holding onto the gears?
Are you sure the wiring is correct? I mean that red-green and blue-yellow correspond to the wiring of the two motor coils? It seems to me like a power issue, but I'm not sure why it would work sometimes and not others if it is.
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