Could you show me the entries from the s2Member logs for these transactions that had a problem? Please obscure any sensitive information.
Does it happen with every transaction or only some? Can you find a common denominator between them? Can you reproduce the problem consistently? If so, could you try reproducing it in a clean WP installation with just s2Member added?
@GDUKMum same for you. It'd be great to isolate what is causing this to happen in your installations, since it doesn't seem to be happening to everyone.
I look forward to your updates.