I know about that particular issue. I've been unable to find a proxy to work with Google to test that hypothesis out (though I might run a check from Chrome while at my doctor's this afternoon), though it does surprise me that I'm running into this via ITA Matrix and it's still popping as an issue.
With that said, running basically the same search on Kayak LAX-BNE as I'm running on ITA LAX-BNE generates some cheaper results.
The annoying thing is that this is, at this rate, likely to lose VA my business in favor of another airline (Singapore or Air New Zealand). $3900 I can work with. $4900 I can justify given the other trip. $6100? Nope.