Automatic branch management disables manually created branches

We are using an older version of Bamboo, 5.6.2 and SVN, and it seems that the automatic branch management disables manually created branches.

Let's say it detects a new SVN branch. It will create the Bamboo branch, but after a few minutes it will disable the other branches that are not automatically managed. The repo urls are valid so I don't think it's a connection issue.

Some manually created branches also re-use the same trunk url because we are using plan variables to build different configuration from the same sources. 

Is this an expected behavior?

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