The SugarCRM upgrade chain is complex. Sometimes there is not an obvious upgrade from the current version to the new version.
The checker correctly detected the avail of Sugar Community Edition 5.5 and 5.5a, but the upgrades have gone badly.
The issue is that there are frequently upgrades to the database, so the upgrade script needs to be run.
When the upgrade script with the SQL is not run, errors like :"Sugar CRM 5.5.0a Files May Only Be Used With A Sugar CRM 5.5.0a Database." result.