The reason is that DV based codecs are the only ones with lower field dominance. So when you tanscode to H264 it is no longer DV which is why when you bring and H264 Quicktime into FCP it is not lower field dominant.
Where are you submitting an H264 file for TX - are you UK based ?
Certainly FCP will usually recognise all codecs except DV based ones as upper field dominant and that is correct. DV is the only codec that is lower field dominant.
For instance, if you were to edit a DV file into a ProRes sequence then the field dominance would be reversed and it would become upper field dominant. I believe the same is true of H264 or indeed any other non DV based codec.