I've reviewed the code but cannot find any reason for the behaviour you see. Does this happen for empty folders only? Is there any chance to post a screenshot of the AWS S3 console of such a folder with 'Versions -> Show' enabled?
We have just released version 6.9.4 which contains a small bugfix for an edge case when working with versioned buckets. Can you please try this version and check if you still see this issue? If yes, I'm still interested in the screenshot mentioned.