Lets say you have two directories in JIRA: a crowd directory and the internal directory. Further lets say you have crowd sso configured in JIRA.

Now lets say you want you edit the crowd directory in JIRA (e.g. change it from read to read/write). You can't do this as a user from the directory because JIRA wont let you. Normally you would login as and admin from the internal directory and edit the crowd directory. However, as the crowd sso authenticator only allows users from a crowd directory to login. This basically means you can't change the configuration of the crowd directory.

The way to work around this is disable crowd sso (i.e. edit seraph-config.xml) and restart JIRA. This will the admin login using a user from the internal directory which will in turn let them edit the crowd directory.