Plenty of chances for field dominance to be screwed up with your workflow. Firstly I presume you shot HDV even though you said “- Filmed the footage in HD on a Sony Z7 (DV-Pal)” and also because you said you captured it into FCP as HD. If that is true, then the field dominance should be set to upper for the captured files.
If you then edited those HDV files in a DV sequence, the shift fields filter would need to be on all the clips as DV is lower filed as you have identified. Then, when you exported the QT file, what codec did you choose? If it was DV then it should be lower. Any other codec should have been upper in PAL.
Have you at any stage seen the sequence or you QT file on an external interlace monitor? If not, then you might have the fields problem baked in before making your mpeg file for DVDSP.