Starting with version 0.15.x, the following limitations apply when using the Plugin with JIRA 6 and the Service Desk Plugin (up to version 2.5.9).

If these limitations are not acceptable for your environment, do not update from version 0.14.7 of the plugin.

These limitations do not apply to JIRA Service Desk 3.x (based on JIRA 7). 

• If the override login-option is active and a SD Customer accesses the JIRA main URL (e.g. https://jira.example.com/), an error message occurs instead of the Service Desk Customer Portal.
• If a Service Desk Customer Portal is accessed (e.g. https://jira.example.com/servicedesk/customer/portal/1), the Service Desk Customer Portal login page is shown.

Workaround:

• Use a link like this to login to JIRA Service Desk: https://jira.example.com/plugins/servlet/samlsso?redirectTo=/servicedesk/customer/portal/1 (replace /portal/1 with the appropriate portal ID)