On why one would want the wheels not to lock up when power is removed, aside from being extremely convenient in operation, I would think the main thing would be that if the purpose of an e-stop button is to prevent accidents, it would be pretty useless to have one that will cause derailments, and possible damage to the engine. Whatever other reasons the ability to press a direction button and have the engine roll smoothly to a stop has been a "feature" of conventional running all the way back.
On speculating about the hardware and software in use, until someone posts any information, even just photos of the boards that can show what is used to control the motors, there is little more that can be done. I can guess as to hardware and/or software solutions that MTH could use, and can guess as to how the problem occurred from using standard design practices. I can also guess about how an end user could solve the problem, but without knowing what the output stage of the ps3 electronics looks like, all I can do is guess.
JGL
Edit: Also, as far as powering motors it wouldn't do much good, but for running the electronics, I'm under the impression that all PS2 and PS3 engines have a battery, so the electronics should have no problem continuing to run when power is cycled.
