Web Support can fix it; my experience is that the phone call took about 20 minutes, but 10 of that was because the fare class I wanted vanished while I was on the phone with Web Support.
My case was cut-and-dry. The ticket cost (let's use approximate round numbers) $350 a/i, I used a $100 e-cert, the price went to $260. Web Support was able to get $250.
This was also discussed last Sunday at
http://www.flyertalk.com/forum/unite...ng-e-cert.html.
The best explanation I read was that someone guessing that FAA taxes are being correctly calculated (and mostly absent) UNLESS you use an e-cert, in which case the taxes get incorrectly calculated as some higher amount.