Which version of zoiper is this ? Zoiper 3 or zoiper classic ?
Is there anything special about the setup ? Is this a standalone windows pc or is a domain controller involved or some sort of remote desktop / terminal server / citrix etc ?
Is this Zoiper Business or the free version ? (The different versions store the configuration in a different place). It will go either into the installation folder or into the %APPDATA% folder.
I believe something is deleting or overwriting the configuration file (or maybe zoiper does not have write permissions to the folder).