Please try using the latest developer's release. It should fix this issue.
With the version Akeeba Backup Professional svn119 (2010-04-21) I get a cron error, but I don’t know if is a site related issue because I didn’t yet tested the Akeeba Backup Professional 3.0.b1 (2010-04-20) on this site.
Here the mail from cron command /usr/local/bin/php /home/ilconven/public_html/administrator/components/com_akeeba/backup.php -profile 2 -description "Backup solo DB"
Akeeba Backup CLI svn119 (2010-04-21)
Copyright (C) 2010 Nicholas K. Dionysopoulos
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Akeeba Backup is Free Software, distributed under the terms of the GNU General
Public License version 3 or, at your option, any later version.
This program comes with ABSOLUTELY NO WARRANTY as per sections 15 & 16 of the
license. See http://www.gnu.org/licenses/gpl-3.0.html for details.
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Starting a new backup with the following parameters:
Profile ID 2
Description "Backup solo DB"
Warning: AEUtilJconfig::require_once(/home/ilconven/public_html/administrator/configuration.php): failed to open stream: No such file or directory in /home/ilconven/public_html/administrator/components/com_akeeba/akeeba/plugins/utils/jconfig.php on line 27
Fatal error: AEUtilJconfig::require_once(): Failed opening required '/home/ilconven/public_html/administrator/configuration.php' (include_path='.:/usr/lib/php:/usr/local/lib/php') in /home/ilconven/public_html/administrator/components/com_akeeba/akeeba/plugins/utils/jconfig.php on line 27
Warning: AEUtilJconfig::require_once(/home/ilconven/public_html/administrator/configuration.php): failed to open stream: No such file or directory in /home/ilconven/public_html/administrator/components/com_akeeba/akeeba/plugins/utils/jconfig.php on line 27