OK, this is probably the 1.000 blog post concering whether to choose MSBuild vs. NAnt.
I had quite a though time fighting my build-environment with MSBuild, after starting out with NAnt (even before MSBee was available). But not I got a couple of things worked out: I can build and do some sort of xcopy-deploymend, I can run NUnit and NCover (even though I had different results from running the gui-runner and the automated nunit-target from my MSBuid-script ?!). But adding more features to this build-process seems be a much bigger burden, that doing the same with NAnt.
So I figured: I will use NAnt for the overall build-process and I will only consider MSBuild for build my solution. I’ll see how this side-by-side usage will work out.