Enable more logging and see what is happening when you stop JIRA. Mostly it will be some plugin which you have installed which is taking time to shut down. Try to disable plugins and then shutdown jira.
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June 11, 2015 edited
Hello Rajiv,
Your log files could give a clear spot about where is the root cause of this problem.
In additional with the community support and if you face some trouble checking your log files, feel free to create a ticket at support.atlassian.com where our Support Engineers can also help you in that case.
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