Firstly registration can be done via script, zac reg http://server
However the certificate prompts for installation twice and as far as I
can tell automation of this yes is not supported.

Before registration prompts for a login during boot. This can register
the agent too which is nice but the prompting for login occurs at a time
when Windows is undertaking an autoadminlogin. This prompting makes it
a nonautoadminlogin.

the work required for image preparation of the agent is not always
successful. The previous two points make the agent impossible to deploy
with an SOE on the image.

Running the agent slows computer startup and shutdown on Vista sp1.

I am using zcm 10.1.1