[Jimmy Cao]

Do you have the 12V, 6V, and 5V lights lit up? If any of the 3 are out, that's a pretty good indication of a short or hardware failure, although the former is more likely).

I know you said your code doesn't seem to be the cause, but it's still worth considering. With the removal of the watchdog, a timeout value was given to each output. If the code doesn't specify a new value within X milliseconds, the outputs time out, which would produce a "no input" signal on motor controllers (The downside of no watchdog is that it's hard to tell this kind of a software problem apart from a hardware problem, at least at a glance). It may be worthwhile to check once more for infinite loops in your code.