UserAgent: Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 Safari/537.36

Example URL:

Steps to reproduce the problem:
1. Attempt to access a domain that resolves to two different IP's based upon the nameserver in use. Let one be an internal IP resolved through a nameserver that's only accessible through a VPN and the other be a public IP that's accessed through publicly available nameservers.
2. Nameservers config from chrome://net-internals/#dns
<internal VPN dns 1>:53
<internal VPN dns 2>:53
<router/public dns>:53

What is the expected behavior?
I'd expect the dns to resolve from internal dns 1 or 2 like dig or firefox do. 

What went wrong?
Instead it will randomly resolve from the public dns. Sometimes it will get it right, but it seems like most of the time it's resolving from the public dns and even clearing the host cache on chrome://net-internals/#dns doesn't seem to help.

Did this work before? N/A 

Chrome version: 55.0.2883.87  Channel: stable
OS Version: 
Flash Version: Shockwave Flash 24.0 r0

I have seen this work correctly in Chrome on OS X and in Firefox on Linux. I feel like this used to work correctly and stopped within the past 6 months, but I'm not 100% sure on that. 
This superuser question seems to almost exactly describe my issue http://superuser.com/questions/656938/does-chrome-use-a-different-dns-server-from-the-os?rq=1