At some point in the wizard you get to select the orchestrations dll which you want to use for generating the WCF service. I had made some changes to the orchestrations project, which I had compiled. But much to my surprise, the service didn't reflect my changes!
Only after I GAC'ed the dll the wizard worked and generated the service as I expected.
Conclusion: even though the wizard lets you pick the dll, it still uses the version from the GAC.