I created a plan where I want to checkout the sources from three different repositories in an alternative sub-directory each.
Bamboo creates the sub-dirs in the working directory but checks out the source code to the working dir root.
As the source dir is cleaned up before checkout I got the sources of one repo only.
Bamboo Version: 5.15.3 build 51515
Source Code Repo: Plastic SCM plugin 5.10.1
UPDATE: issue still occurs with Bamboo 6.3.0
Even if there is only one repo the sub directory option doesn't work. Maybe it's an issue of the plasticscm plugin.