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This is a know issue that is very easy to miss. Usual indicationis if the web parts do not appear after deployment.
It usually means that the user used to launch the wizarddoes not have the access to the SharePoint database, so it’s recommended to usethe same user account that was SharePoint deployed to be used for Web Serverdeployment.
This issue is fixable by increasing the timeout value in SharePoint:
This could be related to SharePoint app pool user change aftert he isntalatio nwas already acomplished. This can be changed by manualy changing BDC object access rights to a required user.