You didn't miss anything. This is the second time I've heard of this issue of FireWire output reversing the field dominance.
Unfortunately, I don't recall a definite cause ever being isolated, or a solution found.
Thanks very much Jim. It's not the answer I wanted but at least I'm not going barmy! Just for the record, exporting to a file, via Media Encoder, is good. It's just the Firewire output.
I have a few questions.
1. If you capture some footage, and then export it directly out again, is there still a problem?
2. If you don't have AVCHD on the sequence does it still do it? (Because AVCHD uses upper first, I believe.)
3. If you export from After Effects, does it stil lhave the problem?
If you want to avoid having to reverse every clip in the timeline individually then you can right click each source clip in the bin and select the "modify>interpet" option and make the field order correct. This way anytime you drag anything from that clip to the timeline it will already be corrected. Doing this with the 1 source clip in the bin will also correct any trimmed clips created from the source clip as well. Basically it will save you from having to click the same clip several times in the timeline to reverse the field order individually.
However it still clearly stinks it's reversing your field order, sorry I don't have any ideas on how to fix your actual problem.