Shopify has had recent problems with duplication. They have since fixed that issue.
I have had similar issues with numerical values changing. Shopify CSV doesn't play well with excel. The most reliable method I have found is to open the CSV file in Open Office and change the columns with numerical values to TEXT type rather than Standard. Then save the file as Microsoft Excel 97/2000/XP. Then I run my excel VBA code or make the edits I need. Then save as a CSV file before uploading.