I can't reproduce your issue. It works for me. It's really strange, because notification scripts use the same method to change time to your regional settings as those methods to show list of alerts and send mails.
You could try to manipulate some data to see time before and after conversion.
Edit file modules/Utils/Messenger/refresh.php
and replace line 34 with this:
print('if(confirm(\''.Epesi::escapeJS(__('Alert on: %s',array(Base_RegionalSettingsCommon::time2reg($row['alert_on']) . "($row[alert_on])"))."\n".$ret."\n".($row['message']?__('Alarm comment: %s',array($row['message'])):'')."\n\n".__('Are you sure you want to turn off the alarm?'),false).'\')) new Ajax.Request(\'modules/Utils/Messenger/turnoff.php\',{method:\'get\',parameters:{id:'.$row['id'].'}});');
You'll get original time from database in parenthesis.
Regards,
Adam
