I have come across this issue a few times. If you create an MSI that has only assemblies in it and then apply it to a BizTalk application, there is a chance that it may unconfigure some of your ports or orchestrations. The reason that this happens is because BizTalk tries to apply a previously used Bindings file which results in your components losing their configuration.
If this is happening to you, navigate to:
{path to Users or “Documents and Settings”}{UserName}{AppData or Application Data}RoamingMicrosoftBizTalk ServerDeploymentBindingFiles
Sample Windows Server 2003: C:Documents and SettingsAdministratorApplication DataMicrosoftBizTalk ServerDeploymentBindingFiles
Sample Windows Server 2008: C:UsersAdministratorAppDataRoamingMicrosoftBizTalk ServerDeploymentBindingFiles
This folder contains a list of bindings files for all of your assemblies. Either delete all of these files or just the ones that apply to your MSI. The next time that you attempt to deploy your MSI, the bindings should remain the same.
