The base URL is set in the System Administration of Jira:
JIRA Administration -> System -> General Configuration
The Base URL should be the main JIRA URL, the main access URL to your Jira.
Set the correct URL under admin -> system -> general configuration
It should be set to the url your users will be accessing the system under. A lot of people run Atlassian stuff behind proxies, but that rule stands - your users will be using a proxied url, so you set the base url to the proxied url, not the url of the JIRA server.
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Or... what Thomas posted before I got there, too
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