Hey guys,
Sorry, I should have updated the thread when I fixed the problem.
Turns out that when the DV footage was put into an HDV sequence by mistake, FCP ads a “shift fields” effect to each clip to make the DV material comply to the HDV field order.
When I changed the sequence property to put it to DV, FCP is not smart enough to remove those effects, so the field order was indeed wrong. I had to go into each clip and remove that effect.
After that, all was fine.
Thanks everyone for your time and suggestions. Much appreciated.