Are you importing the file through our web UI or through the API or an integration using the API? If you're using the API, is there any chance you can email us the file you're importing and your username to our API support email of firstname.lastname@example.org so we can take a look?
As noted in the linked thread, we have found a bug in the v1 bulk API that does indeed cause duplicates to be created. We are investigating this and hope to have a fix soon. We have also confirmed that this is not an issue with any integrations that have upgraded to our v2 API.