Now JIRA will not load - the following extract from the error from the stdout log seems most relevant:
2011-08-31 14:46:17,337 Finalizer WARN [core.entity.jdbc.SQLProcessor] Already closed.
2011-08-31 14:46:17,415 main INFO [atlassian.plugin.util.WaitUntil] Plugins that have yet to be enabled: [com.atlassian.gadgets.embedded, com.atlassian.gadgets.dashboard, com.atlassian.streams.streams-jira-plugin, com.atlassian.jira.gadgets, com.atlassian.jirafisheyeplugin, com.atlassian.gadgets.directory, com.atlassian.jira.rest, com.atlassian.gadgets.oauth.serviceprovider, com.atlassian.gadgets.opensocial], 57 seconds remaining
2011-08-31 14:46:18,525 main INFO [atlassian.plugin.util.WaitUntil] Plugins that have yet to be enabled: [com.atlassian.gadgets.directory], 56 seconds remaining
2011-08-31 14:46:20,728 main INFO [atlassian.plugin.loaders.ScanningPluginLoader] No plugins found to be deployed
2011-08-31 14:46:21,712 main FATAL [atlassian.jira.upgrade.ConsistencyLauncher] A fatal error occured during initialisation. JIRA has been locked.
com.atlassian.jira.InfrastructureException: Error occurred while starting Plugin Manager. Unable to esablish a connection with the database. (Network error IOException: Connection refused: connect)