Careful, this is a answer only for your edit
I don't have answer but i have the same problem. I suspect that the problem come from the account used when installing agent, a wrong environement variable. because environement variable are not the same between a administrator account or user account.
you can try this installing agent with the parameter /work_dir="path to directory", maybe it solve the problem.
Personally, for the plugin, i bulid 2 packages, one for x32 and another for x64, and i deploy it with server. It allows me to update plugins like i want without uninstall/reinstall agent.
i you found a solution, please tell us
PS : Sorry, for my bad english, i'm a french frog ^^