The documentation for the alternative method of upgrading Jira 3 to Jira 4-the method of pointing the new installation to the existing database-needs more information regarding the new Jira Home setting.
Or, the upgrade process needs an additional task added to correct the index and attachment paths in the property tables.

After the upgrade completes, the attachments directory and index files are still located in the old Jira locations according to the jira.path.attachments and jira.path.index values in the propertyentry and propertystring tables that are carried over from Jira 3.
It disregards the jira.home value in the jira-application.properties.

In testing the upgrade, I have discovered that before I start up our Jira 4 for the first time, that I need to run the following SQL to force my home directory to completely move from /usr/local/jira to /data1/atlassian-jira-enterprise-4.1.2-standalone/home.

-- Change the home directory settings
insert into propertyentry values(10010, 'jira.properties', 1, 'jira.path.index.use.default.directory', 1);
insert into propertyentry values(10011, 'jira.properties', 1, 'jira.path.attachments.use.default.directory', 1);
insert into propertynumber values (10010, 1);
insert into propertynumber values (10011, 1);
update propertystring set propertyvalue='/data1/atlassian-jira-enterprise-4.1.2-standalone/home/data/attachments' where propertyvalue='/usr/local/jira/attachments';
delete from propertystring where id in (select id from propertyentry where property_key in ('jira.path.index', 'jira.path.backup'));
delete from propertyentry where property_key in ('jira.path.index', 'jira.path.backup');

When doing the same thing upgrading Confluence 3.0.2 to 3.3.1, the index and attachment directories respect the new confluence home directory.