I have a web application in an Azure cloud service using ADFS 2.0. I wanna add others parties identifier, like Windows Live Id. The web.config includes a connection string encrypted with the asp.net_regis utility. When I deploy to the cloud service without the new identity provider references, it works fine, but when I add these new references, I'm getting this exception: The section is marked as being protected, but it does not have the correct format. It should contain only the <EncryptedData> child node. I have included the certificate I used to encrypt it in the Token Decription tab in ACS portal. Why I'm getting this error?
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Is this error coming from your application, ACS, or your identity provider? When you say you had it working with ADFS, this was connected to ADFS directly or via ACS? – Oren Melzer Feb 18 '13 at 21:10
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Before the update was connected to ADFS. If I add the FederationMetadada from ACS as STS Reference in the project, the application throws this exception in the log. – Jorge Feb 19 '13 at 09:15
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See if any new keys have been added (or any other elements for that matter) between the nodes because it will cause this error. May be you have transformations applied while deploying.

Danila Polevshchikov
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Yes, I have compared the thumbprint of the certificate used for encrypt the web.config with the one in ACS and realized didn't match, the problem here was we have different certs with same name within the team. Thank you! – Jorge Feb 25 '13 at 15:50