Here is the step to reproduce the issue:

1. Install a fresh JIRA 6 instance.
2. Create a second "user1@test" then rename it to "user1".
3. Create a new issue security scheme with one security level limited to admin user and "user1".
4. Create a new project and one issue with the security level.
5. Logout and login with the account "user1" then open the issue.
6. The Permission violation page shows up.

Please note that the issue only affected the security level or project permission created after user renamed.

As a temporary workaround solution: It is possible to create a customfield with type of user picker and associate with the issue security / project permission, then add the user name in the customfield. As only the user who got the edit issue permission can edit the field.