So very sorry for this late reply. This post got flagged for spam and a e-mail error caused the notification to not get sent.
There is one circuit ground that is shared by all the ADCs, DACs, Triggers, and GPIO lines. This ground is isolated from the power supply and the case by an inductor. For the back-panel USB, the USB signal ground is connected to circuit ground, but the USB shield is very weekly connected to the case. For the front panel USB (not yet supported in software) the USB signal ground is connected to circuit ground and the USB case is connected to the Quarto case ground.
I hope this answers your questions, but please post back if you have any more questions. And again, I am very sorry for the incredibly late reply. That was major IT failure on our part and I'm sorry.