This is bug we identified in 5.X version of bamboo. Whenever you change permission used for your reposiotry connection. You need to refresh the repository configuration even there is no change.
Go to link repository and open linked repo and click on save even thought there is no any change.
Samething u need to do for Plan–>Repository. Just click on save button, even though there is no any change.
Then your plan should works fine.
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