The following documentation specifies that the jira.search.views.max.limit setting is disabled by default:

http://confluence.atlassian.com/display/JIRA/Limiting+the+number+of+issues+returned+from+a+search+view+such+as+an+RSS+feed

However, the setting is specified in the WEB-INF/classes/jpm.xml file that ships with JIRA 4.4.3 and 4.4.4 (and possibly other 4.4.x releases).

<property>
    <!--
        Whether search results are capped to a hard limit, otherwise return a 403 (Forbidden) to the client.
        Set this to negative (-1) or empty for unlimited results.
        NOTE: this must be EQUAL TO OR GREATER THAN jira.search.views.default.max above, otherwise all Issue Navigator links will fail with a 403
    -->
    <key>jira.search.views.max.limit</key>
    <default-value>1000</default-value>
    <type>uint</type>
    <user-editable>false</user-editable>
</property>

This is particularly troublesome when upgrading from pre-4.4 releases, since this represents a change in behaviour for users that is difficult to notice during the upgrade.

The documentation has since been corrected but kavian is now suggesting that we should consider changing the default value in this to be greater than what it currently is or reduce the default value of jira.search.views.default.max