It seems that JIRA does not always remove the jira-home lock file when the WAR edition is stopped/restarted.

A number of users have reported that the jira-home lock file is not always removed when they stop and restart JIRA WAR edition in various App Servers.

I think we need to investigate this for all supported App Servers.
Also look into the difference between stopping and restarting JIRA with the App server up, and bouncing the actual App Server.