According to the release notes, Stanza 2.1 "removes the ability to share books over USB as required by Apple"
I'm not sure what this feature refers to-Stanza never had an official way to transfer books over USB that I knew of besides using iPhone Explorer, a third party app.
Anyways, if you do use USB with Stanza, don't upgrade without checking it out.
edit: ok, Lexcycle updated their FAQ
-it IS the iPhone Explorer method they had to deprecate. That is a pity, I know some people don't have wireless.