After installing patch "3.13.4 patch-JRA-21004-3.13.4.zip" from http://confluence.atlassian.com/display/JIRA/JIRA+Security+Advisory+2010-04-16, we noticed that links were no longer start with issue key.
The links were in form of " title="

.

Making this change seem to fix the issue.

diff edit-webapp/includes/snippets/issuelinksmall.jsp webapp/includes/snippets/issuelinksmall.jsp
7c7
< <font size="1"><a href="<webwork:url value="'/browse/' + string('key')" />" title="<webwork:property value="string('summary')" />">
—
> <font size="1"><a href="<webwork:url value="'/browse/' + string('key')" />" />" title="<webwork:property value="string('summary')" />">