Hello @matthew_boddie,
the v40 patch you mentioned is v40.10, isn’t it? I think you were impacted by this issue, which was solved in v40.11. So you have two options to workaround it:
- Update to 3.3.1, which has a workaround for this issue.
- Keep version 2.9.1.1 and update the server to v40.11.
Regarding the flattened orgunit tree, it was an intentional change because there were complaints about having a very big OU tree. But now it seems that the solution is not working in some cases, so it seems that we need to look for a better approach (see also this ticket).