We were evaluating JIRA Service Desk, and it was working fine, but once we purchased and installed the license, Service Desk prompted us to "Migrate Permission Scheme", which associated a new permission scheme with the project. Afterwards, external users were unable to log into the Customer Portal. They get a permission denied error.
Turns out it was the licence I got when I purchased the plugin. The evaluation licence was a version 2 licence, but the one I received was a version 1 licence. The v1 licence reconfigured my service desk projects which were initially setup with a v2 licence permission scheme.
The Akkadian support team were fantastic, They quickly found the root of the problem and got me a new licence.
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