I think this is caused by the way resolvconf treats local nameservers. Checking the man page, I noticed this:
If set to "yes" then the libc script will include no more nameserver addresses after the first nameserver address that is a loopback address. (In IPv4 a loopback address is any one that starts with "127.". In IPv6 the loopback address is "::1".)
The advantage of truncating the nameserver list after a loopback address is that doing so inhibits unnecessary changes to resolv.conf and thus reduces the number of instances in which the update-libc.d/ scripts have to be run. When an interface is brought up or down the local caching nameserver that listens on the loopback address is still informed of the change and adapts accordingly; the clients of the resolver which use the local caching nameserver do not need to be notified of the change. A disadvantage of this mode of operation is that applications have no secondary or tertiary nameserver address to fall back on should the local caching nameserver crash. Insofar as a local nameserver crash can be regarded as an unlikely event, this is a relatively minor disadvantage. Set to "no" to disable truncation. The default is "yes".
A deprecated synonym for this variable is TRUNCATE_NAMESERVER_LIST_AFTER_127."