Another possible and powerful replacement would be Topics by Chio (
www.websitebaker.at) but that does not solve your issues. They are related to the server configuration.
My guess at the moment is, that you can not let your webserver create files / folders within the WB installation. The files of WB have been uploaded by FTP, right? You need to find out, if your FTP useraccount shares a usergroup with the user the webserver is running (lets call it Service Useraccount). Depending on that you may set your accessrights on the files / folders.
A bit more information can be found here:
http://www.websitebaker2.org/topics/files-and-permissions.phpcheers
Klaus