This is an annoying quirk I found when having multiple Biztalk applications running on the one server. I created a little app, built it and tried deploying it via the Biztalk WCF Service deployment wizard - when prompted for the application to deploy to, i specified the biztalk app container i had created in the BizTalk Server Administration console earlier and finished the wizard. The wizard completed sucessfully but i found myself puzzled as to why, when i went into the console and clicked on Orchestrations, my Orchestrations didn't appear, huh? The wizard hadn't thrown any errors?
In addition to specifying the App container to use in the WCF Service Publish wizard, you also need to specify the Biztalk Application Container in the properties of the biztalk project at the Visual Studio end - right click on the project in the Solution Explorer and choose the 'Deployment' tab in the page that is displayed:
Make sure the Application name matches the same name of your Biztalk Application and try redeploying via the wizard and your orchestrations should now appear as expected.
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