Thank you for your reply.
Please make sure that you checked specific store view during import and un-checked 'Default values':
http://screencast.com/t/bcdX2N7ldfE
Also, please make sure that you used Category id as identifier.
If the issue still remains, please contact us via e-mail at:
http://support.emagicone.com/submit_ticket
and provide us with the following details: your store connection configuration (you can save it at Preferences[F12] / Actions / Save current configuration), import configuration (you can save it at the last step of import wizard), .csv file so we could check what caused the issue for you.
Waiting to hear from you