Thank you for your reply.
Can you please submit a ticket at:
http://support.emagicone.com/
and provide us with Store Manager logs to check (you can find log files at Start/All programs/eMagicOne/Store Manager for Magento/Application data/Logs)
Please note, that Magento does not allow to apply Categories ids, so we do not recommend you to import Categories by ID as identifier (it could be used only if you are updating Categories at your store using the file that was created from your database).
Waiting to hear from you