I don't use virtual Copies.
This Bug only exists when exporting many files - round about 100 or more.
What are the file names for the duplicate pairs, are they in the same folder or in a subfolder, do you have 'Show Photos in Subfolders checked, did you shoot some images with your camera set to JPEG + raw format? More information is required to determine the cause of the duplicates. Screenshots would be helpful. LR does not export duplicates so there's something else going on here.