The duplicates you are saying about custom fields is actually not duplicates but that is the core feature of VirtueMart. For a child product, there are two custom fields shown on backend when parent product has its own values set for these custom fields. The custom field that has options of o and d with check boxes is for the parent product. Where d means deactivate or disable, when this checkbox is checked the parent value is not used on the child product. If o is checked which means override, the parent value will override the child product value.The other custom field without any of these checkboxes are the actual custom field of child product.
The checkbox disinh: with child product custom field is a new feature added by VirtueMart in the latest version. We are looking into this feature and will be adding support in our upcoming RO CSVI version.
Please post import debug log and sample of your import file to check. Also post screenshot of your custom fields and on the duplicate issue. To get the debug log check How to get debug information? document.