I've noticed the same exact problem just recently. I know bhawver mentioned the aclient.inp, but he misunderstands what you are asking.
I also install the agent post sysprep with the same script I use to install it for the first time on a machine: c:\dagent\dagent_x64.msi /quiet server_tcp_addr=172.17.1.40 server_tcp_port=402 scripted_install=1 LAUNCHUI=FALSE
This has worked totally fine in the past, before my SP3 to SP5 upgrade. The DAgent would install, contact the server, and then take the "Windows Agent Settings" (most importantly the "Allow Remote Control").
This is no longer working. I do have the "Force new agents to take these default settings" option enabled, but it has no effect. The DAgent communicates with the server fine, but it's not updating with the Default Settings.
I could use an .inp file if I have to, but that's not the way it's designed to work - it specifically says, "You can force all new agents to take default settings the first time they connect to the server, even if they were installed with custom settings using an input file."
I'm wondering if Windows 7 is somehow blocking the update?