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?