Crowd Embedded was introduce in JIRA 4.3.x making the full integration with LDAP now available in the JIRA install itself, avoiding the need of integration with a external Crowd instance. In other hand, during a upgrade from previous version to JIRA 4.3.x if users management was once delegated to external Crowd and this integration is removed, users are not migrated to JIRA internal user database.

Atlassian does not provide a path to migrate user information from Crowd to JIRA during the upgrade. This is by design. If you previous installation of JIRA was integrated with Crowd, all users, groups and membership information will be saved on Crowd database. Therefore if during the upgrade the external instance of Crowd is not available or if upgrade notes for Crowd integrated were not follow, JIRA will NOT recreate the users locally.

Workaround: http://confluence.atlassian.com/display/JIRAKB/Migration+path+from+Crowd+to+Crowd+Embedded+during+upgrade+to+JIRA+4.3.x