Hhmm... Can you check again about that resetting behavior? What I've seen is that the parameters stick even across a power down, and the controller is locked out only when ZS is running. No problem with setting rail speed using the Config button when ZS is not running, and the setting holds for ZS. (Yes, rail speed will be exposed as a parameter inside ZS in a later version.)The one thing I'm having problems with is setting other parameters such as rail speed via the hardware controller. Reconnecting the USB seems to reset these parameters and the controller is locked out when the USB is connected.
I have no experience with the 5D Mark II. On my T1i, the required trick is to initially trigger Live View using the button on the camera back. Check also in EOS Utility for a setting that enables camera controls as well as computer controls. I don't think that one is mentioned in the documentation, but I have vague memories of running into it at some point.In addition, I'm using live view on my Canon 5D mark II (via USB) in combination with the Stackshot shutter cable. Using these together stops the StackShot camera trigger from working the shutter on the camera. I'm therefore not sure how to fire the camera via the StackShot in live view.