We need to check the issue from our side. Thus, we need some details from you to try to reproduce the issue and find possible solution.
Can you please send us your request here -
http://support.emagicone.com/submit_ticket
and provide us your import file, import configuration (it can be saved at the last step of import) and your store configuration file (Preferences - Actions - Save current configuration).
We will investigate what can be wrong, reply you back and also post result here for other users who face similar problem.