acondit: Are you planning on running this from emc? Pluto maybe? mesa? I don't remember what you where planning.
I think the way the uP on the uhu worked is it actually ouput pwm/not-pwm. The pluto or even the software pwmgen doesn't ouput an anti signal on the opposite pin while the other is generating pwm. (hope that made sense).
So if you look at your circuit if the right side of the bridge goes into over-current (trips the flip flop) it will not get reset until there is a left side pwm rising edge. This is why I or-ed the two pwm signals into the flipslop
http://www.electronicsam.com/images/...schemfinal.PNG
^ the logic was breadboarded and 'seems' to work.. But I have not found the time to make a board yet.