Well it turns out the explanation for my problems with repeating this cut are due to a bad motor.
Funny thing when I first got the machine, I had real difficulty plunging plywood and polycarbonate. Trying to drill holes didn't work and someone told me drilling is difficult. So I switched to a smaller bit and profiled my holes, figuring that as long as it worked, I was okay with it.
So last night I'm trying to cut the polycarbonate pretty much exactly as I had before, using the same feed/plunge rates and only unsure of my motor speed (trying the DW611 at 3 and all the way up at 6, etc.). And I am just dropping steps like mad.
So this morning I'm trying to adjust the plunge rates, etc., and not getting anywhere, still dropping Z steps like nuts, and then I just start to cut air and see the motor isn't reliably moving the Z-axis. So I start jogging and see the same thing, it is just getting worse and worse.
So I try to turn the shaft of the Z-axis motor and sure enough, it spins easily (it should be locked, the machine is powered-up. So I unplug the power and swap the X and Z axis connections to the controller board and power back up, and the Z still won't lock (so I know it isn't the controller board).
So it looks like my Z problems aren't over yet.
I sent an E-Mail to email@example.com, hoping they can sell me a motor.