the Jira soap api is missing a parameter when using the createUser function. With the introduction of the new user directory management one must define the target user directory when creating a new user. Unfortunately without the missing parameter for the target directory, users that are created via SOAP will only be created in the primary user directory.
Which is in our case a read only ldap directory.
http://docs.atlassian.com/software/jira/docs/api/rpc-jira-plugin/latest/com/atlassian/jira/rpc/soap/JiraSoapService.html#createUser%28java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String,%20java.lang.String%29