Thanks for getting back to us. Unfortunately we haven't been able to test Flight Compute with an account of that era.
Your hunch sounds like a good one -- it's possible that DNS configuration may behave slightly differently within an EC2 Classic-capable account. We did have a theory that it might have been related to DHCP option set configuration, but our testing ruled that out.
If you do end up determining what configuration within your EC2 Classic-capable account is causing problems, please let us know and we'll take a look at fixing it.