I came across this problem ages ago when trying to deploy an assembly containing orchestrations during our automated build process. When deploying the application we would get the error shown in the below error message.
My first thought was there are no bindings this is a new application being deployed because my msbuild process would clean up/delete the old application before it removes it.
At the time I think id fixed it without really realising what I'd done and just got on with things (I think I'd updated the version of the assembly) and the build process just continued to work. Id also been unable to recreate the problem.
This week the problem came up again so I spent a little more time looking into it. A bit thanks goes out here to James French who commented on a post by Neil Thompson about this.
To quote James the problem is
"On deployment the deployment program which is run by Visual Studio creates/updates one or more BindingInfo.xml files in the folder C:\Documents and Settings\[user name]\Application Data\Microsoft\BizTalk Server\Deployment\BindingFiles. There are two versions of this file depending on whether you are deploying to a new application or are redeploying.
If you deploy a new application the file is created based on reflection of the Assembly which contains the orchestration and is prefixed with a ~ (tilda) character.
If you re-deploy an existing application the binding file is created based on the binding info held in the BizTalkMgmt database for the assembly being published. This file does not have the ~ (tilda) prefix.
The deployment process attempts to apply these bindings after (re)deployment.
I have found that by deleting the Binding.Info.Xml files in the temp folder as well as deleting the Application via the BizTalk management console that the above mentioned error no longer occurs because the deployment program always uses a fresh binding.info.xml file based on the assembly and not what was previously in the database. (PS: Note that I am developing on one machine and deploying onto a second machine)."
Cheers saved me a lot of hassle here!