WPF markup compilation pass

I am trying to manually control the two markup passes in msbuild for
WPF applications. We'd like to use WPF for upcoming applications, but
our build system does not allow msbuild for compilation and linking.
As a solution I'd like to start the two markup compilation tasks in
msbuild manually, with a temporary C# compilation in between. I have
had some luck starting these tasks with the /t:MarkupCompilePass1 and /
t:MarkupCompilePass2, respectively (and a few other, preparatory
tasks). Between them I compile the code with csc. However, the
second markup pass does not generate the BAML.
When I instead use a stripped down project file (XAML files only), and
run msbuild on that project (once before, and once after the temp.
compilation), things work. That's somewhat messy, though.
Does anybody have an idea how I could control the two markup compile
passes with command line parameters?
Thanks,

IndyStef