I use usergroups within the custom directory since several years and have never had any issue with them and I have never noticed similar topics here in the community. Maybe bbt could give some hints.
I have observed this problem in version 11.20.12860.0
Here is what I think is happening.
When you open the management Console I believe it is caching a version of this file.
This file holds all custom users and groups.
The problem arrises when you have multiple administrators.
When they open the management console and add users.
Then they are updating a cached version of this file(CustomDirectoryData) which may have been updated by another administrator.
As a workaround, I ensure that I kill all IE sessions on my server before I add users. Ive not seen the problem since.