It is possible that this is the same issue as #651827. The issue there is that no update is run at boot, so if your system only uses the base file (and no interface configurers, e.g., ifupdown, dhclient, are run) then your dynamically generated /etc/resolv.conf will be absent.
If you think that this may be the same issue, please test the patch I supplied in #651827, or do the following: In the "start" part of the case statement in the resolvconf init script, insert a resolvconf -u line between the resolvconf --create-runtime-directories line and the resolvconf --enable-updates line. Please let me know whether or not this solves your problem. -- Thomas