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You'll need VIEW DEFINITION permission for Compare to work properly. The required permissions are documented at http://documentation.red-gate.com/display/SC11/Permissions+required+to+use+SQL+Compare.
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I have a QA and dev environment. I ran the sql compare and it found a lot of difference I did not know existed, however it also shows that I have a bunch of objects that only exist in one environment or the other. Some of these are legitimate. However, the bulk of them are stored procedures, I was wondering if this might have something to do with permissions as only have read permissions on the QA environment.