Can you provide steps to duplicate the issue? We've never setup the cPanel Extended module for testing since it was developed by ModulesGarden, and is not released with Blesta. You may want to ask ModulesGarden about this issue as well, and see if they have a solution for you. From just glancing at the code, it looks like it should work--but then again, that's usually the case.
If you're willing to update the module itself and test a possible solution, try to update /components/modules/cpanelextended/cpanelextended.php (line 1679) and change:
if($api->sendApi1Request("Ftp", "passwdftp", array('user' => $post["username"], 'passwd' => $post["password"])))
to
if($api->sendApi1Request("Ftp", "passwdftp", array('user' => $post["username"], 'passwd' => $post["ftppassword"])))
You'll need to test this change.