I'm thinking that turning off the updates is a "by design" sort of thing from Microsoft. Because you are running sysprep with the /generalize switch (which is what you should do) Microsoft is clearing a lot of things to make the image more "generic" and function on any number of machines and potentially different environments or use cases. I think changing the update setting qualifies as something they are "resetting". It especially makes sense considering OEM deployments. OEMs create their image to ship out on new computers (with all their "value added software and such) and then they use sysprep to prep the image for other machines as well as influence the OOB experience their customers get. Because that computer could end up in any number of environments, they have to defer/allow the end user to select the option, so Microsoft resets/clears the option - effectively turning it off.
That is a bit of supposition on my part because I can't find official documentation indicating that is the case. At any rate, I'm glad you found a way to address your use case. I'm also thinking that Tom's idea might prove useful as well if needed.