No, restarting and rebooting makes no difference. If the root servers don't know the answer, then the domains simply cannot be seen. It is a problem I have been aware of for years, but never quite put my finger on until now. Moving websites around from one server to another is not the kind of thing people do often, unless it happens to be the kind of thing they do, if you know what I mean (i.e. YMMV).
SME is respecting the TTL entries for your domains. My guess is that the TTL is set to days.
The only reason SME would lag your ISP DNS is if that ISP is hosting the domains in question. If this is the case, then the ISPs DNS would be the authoritative name server for that domain, therefore the change would happen instantly (or as soon as your ISP updated its dbase internally). TTL would not come into play when query their name server directly.
The root name servers have no idea what the IP addresses are for your domains, because they aren't responsible for your domains. They only know where to tell the query to look next for the answer. You might end up with 2,3,4+ hops between name server, starting at the root name server, before you get an answer.
The SME Server setup sequence does provide a box to enter a *single* DNS server if required (up to four would be more appropriate IMO). If the server uses DHCP to get its public IP address, then I think there should be an option to allow it to get the DNS servers that it should use too.
You're looking at SME Server as if it were a regular workstation. There is no need for it to pull name servers from DHCP. SME has its own DNS.
The DNS entry in the SME setup is really meant to specify a DNS on your LAN that provides DNS for the hosts on your LAN in addition to forwarding requests to the internet. Most small to medium sized businesses (users) don't have, or need, multiple DNSs on their LAN, so providing an option for multiple local DNS servers would probably rarely be used.