Atlassian connect jira api returning 401 for a single installation

I have built an atlassian connect based Jira app which is functioning well for the most part, except for a single installation which is unable to authenticate.

Looking through the data, this installation differs from the others where it’s customer dmain is on instead of and it’s client key appears to contain the base url instead of a uuid.

Might someone be able to point me to some documentation or a forum post that details how to deal with these differing installations ?

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