I’ve been having a similar problem. One of my blogs has been showing zero hits for months now, even though I know people are visiting it. The stats plugin works fine on my other two blogs, but not this one:
http://www.celticharper.com/blog/
Both my ww.wp.xz.cn blogs are updated regularly (my one wordpress.com blog updates automatically obviously), and all have the most up-to-date stats plugin – and the .org blogs are generally both upgraded at the exact same time. Stats work fine for one, but not the other.
So what do you do if you already have the stats plugin installed and activated (which I do), and it’s still showing zero hits? Uninstall it and install it again from scratch?