It sounds like a different bug to me, if changing networkmanager fixes
it without changing dnsmasq.  I would file a new Launchpad bug with all
the details you can provide.  You can add a comment to this issue with a
link.

In particular, please specify:
* If you're using IPv4 vs. IPv6
* If you have checked or unchecked the "Use this connection only for resources 
on its network"
* If you have this checked, try unchecking it and see if that makes a difference
* When you say "DNS lookups" please be clear about whether the hostnames being 
looked up are public (e.g., www.google.com or whatever), on your local LAN, or 
in the network accessed via the VPN.  Does it make a difference which one you 
choose?
* Are you using fully-qualified hostnames, or relying on the DNS domain search 
path?  Does it make a difference if you do it differently?

FYI, if you choose "Use this connection only for resources on its
network" then different DNS lookups going to different servers is
expected: the decision is made based on the DNS domain name; lookups for
hosts with domains that are served via the VPN (as determined by
information obtained from the DHCP response when you got an IP address
over the VPN) will be sent to DNS servers in the VPN (again, based on
DHCP).  Lookups for hosts with domains that are not registered by the
VPN will not be sent to the VPN's DNS server.

I assume (but have not tried) that if you don't check that box then all
DNS lookups would go to the VPN DNS servers.  However, this does mean
that no local LAN hostnames can be resolved since your local DNS server
will not be consulted.  It also means if you have multiple VPN
connections going, only one of them will have DNS available.

If you either use fully-qualified hostnames, and/or you ensure that the
VPN's DNS domains come first in the search path, then I don't think
there should be a security issue (unless you don't trust your normal DNS
server, but that's an entirely different situation).

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https://bugs.launchpad.net/bugs/1639776

Title:
  name resolution (dnsmasq) fails to send queries out after
  suspend/resume reconnects the interface

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