Working with Sony XDCAM EX 1080i50 footage on a native timeline, then exporting to a DV25 clip, we have an issue where the fields are correct on the master shot, but cover shots on layer 2 have inverted fields. The original XDCAM timeline has no field issues.
In the 25 frame world DV is the only lower field codec. I would avoid that codec for many reasons but especially as you clips will all need the shift fields filter in a DV sequence. Try ProRes 422 as you sequence codec and everything remains upper field