Dan
There are parts of your question that I do not understand. Let me address the part that I think I do understand and if my answer does not resolve your question then perhaps you can clarify.
When you say tunnel interface am I correct in assuming that we are talking GRE tunnel rather then VPN tunel or something else?
With GRE tunnels the IOS will show the tunnel as up up as long as the router has a viable route to the tunnel destination (unless you have configured the optional GRE tunnel keepalive).
If the serial interface is showing up/down then that is not cosmetic as far as the serial interface is concerned. It means that keepalives have failed on the serial interface and that no traffic is being sent over the serial interface. It may or may not affect the tunnel that the serial interface is not working. As long as there is a viable route toward the tunnel destination then the tunnel itself may work. If I understand the end of your question it does seem to be saying that traffic is going through the tunnel. Am I correct in understanding that?
HTH
Rick
HTH
Rick