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bbfa235
(Get the code!)
This possibly arises from bug #1003842.
What is possibly happening: the second or third nameserver on the list of available nameservers supplied to dnsmasq replies quickly to dnsmasq's query with a negative answer and dnsmasq immediately passes that negative answer back to the resolver.
When dnsmasq is not used, the resolver tries the first nameserver on the list first, only trying the second nameserver after a timeout period.
If this is the problem then the "correct" solution is to fix the malfunctioning nameserver or to remove it from the list.