I recently upgraded JIRA from 4.2.3 to 5.1.7 and everything was fine. I copied the OSUSER.XML file from 4.2.3 to 5.1.7 since we integrated LDAP with JIRA. However, when I later changed the LDAP user password no one could log in. I could log in with an internal (non-LDAP) account, just not accounts that use LDAP for authentication.
After verifying and reverifying the password entered into the OSUSER.XML file was correct, I eventually had our network administrator change the password back and everything worked fine.
The last time I changed the password we were running 4.2.3 and changing the password was not a problem.