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Thanks for your question - Yes, there is a way to configure SQL Source Control to ignore user permission differences
Please see the following post that details how to set the comparison options that SQL Source Control uses when comparing databases to version control:
http://www.red-gate.com/MessageBoard/vi ... hp?t=14278
Using the mechanism specified there, you should be able to set the option for "Ignore users' permissions and role memberships".
Please let us know if you need any further help with this.
Best regards,
Redgate Software