OK, got it. None of these boards will be as clean as U180 is due to its higher integration, so it's worth looking at things like this. I doubt you will see any difference, but it will be very interesting if you do.
Also, wanghar: Wow, you went to the ADG734's! Nice looking board, too. It's very curious that it seemed to help. I found the 788's to be a huge pain when routing, partly due to the thermal pad being in the way, to the point that the space-savings wasn't as great as hoped. (Actually, I wonder why a thermal pad is needed with these sub uW switches - did you use and ground them?) The 734's are much easier to design with, and far easier to hand-solder if necessary.
One suggestion: The decoupling caps need to be right on the supply pins, especially for the CPLD. You seem to have some either absent or somewhat further from the pins than optimum.
What are you referring to by "the current compensation circuit on the A3 board," the input FET modulation? Something else?