This all happened because of one thing - time difference - on 01JUL AU time, the new fares took over, and the old fares had an expiry of 30JUN. When the new fares were rolled out, US based OTA were all still correcty publicising the fare levels as they were within the booking date range. The issue then comes when booking, the OTA verified the fare (check) and queried the airline for current taxes (check) - though these taxes were indeed post fuel tax being migrated over to the fare component, and hence way way lower. The way i read it they were always screwed for that 14 hour time difference, and should honor the ticketed fares. (Yes i am a TA, and was aware of the fuel fine migration on 01JUL, but also gave them clearly undue credit for what they should have been on top of - and avoided this sh**storm)
Just my 2c.