Not saying you’re not having a problem. I just set up a field group on a test site that only had ACF 4 installed, did the upgrade to 5 and did not see any duplication of fields.
Some questions
How did you import your fields into the test site you mentioned?
After activating ACF5 did you get a message that you needed to upgrade the database? If you don’t recall can you try it again and let me know.
