I believe I have found the cause of this bug within nm-named-manager.c.

Should Network Manager fail to update the resolver via the resolvconf
script, then it will fall through to the default behaviour (ie write
details to a temp file and then overwrites /etc/resolv.conf). The code
treats /sbin/resolvconf not being installed in the same way as it would
treat execution of resolvconf failing, which is why we have this problem
of NetworkManager sometimes overwriting the configuration.

I can think of two solutions to this problem.

1. If we find /etc/resolv.conf is a SYMLINK, follow it and update the target 
file.
2. Ignore resolvconf failures, if /etc/resolv.conf is a SYMLINK

I think option 1 is preferable, as it is least likely to leave you without a 
functioning resolver. 
I have patches for both methods, and I will upload them shortly.

Cheers,
Mark

-- 
Network Manager 0.7 doesn't use resolvconf to remove nameserver info if it 
didn't use resolvconf for adding its nameserver info - wipes /etc/resolv.conf 
link
https://bugs.launchpad.net/bugs/324233
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