Comment 6 for bug 497258

it's likely binfmt-support for mono-handled binaries. Either it's needed to run some binaries during installation, in which case vmbuilder should handle binfmt-support specially by stopping it after installation of packages, or it's not really needed and vmbuilder can just avoid it from starting.

mono-runtime just does "update-binfmts --import cli" so I'm a bit surprized that this would actually enable the module in the kernel, it's more likely "invoke-rc.d binfmt-support" start loading them from binfmt-support.postinst, but I thought vmbuilder disabled invoke-rc.d services:
    def prevent_daemons_starting(self):
        os.chmod(self.install_from_template('/usr/sbin/policy-rc.d', 'nostart-policy-rc.d'), 0755)

Could you run vmbuilder in debug mode to see that this occurs after "Preventing daemons from starting" and before "Unpreventing daemons from starting"?