I went through and checked all the things you listed above, and went ahead and applied the shift fields filter, compressed and burnt off to a DVD and it works perfectly, thanks for that!
So am I right in assuming that every format in PAL uses upper field dominance, except for DV? And just to make sure dominances always match in a timeline, then I shouldn’t have any problems? Or is this just for TV? Would it be a different story if I was outputting to web?
Thanks again for your help, best explanation of the problem I’ve seen.