I recently read about a problem, in the Dynamics CRM forum, encountered when trying to import a Dynamics CRM Online customization file to a Dynamics CRM On Premise installation. The error reported was "Either the file could not be uploaded, or this is not a valid Customization file".
It appears that this is a known issue and Microsoft released the details for the fix in KB article 949256. You need to first convert the Online Customization file to a CRM 4 customization file in order to successfully import to the On Premise implementation. It is important to read and follow the instructions carefully in order to resolve the issue.