In PAL everything except DV is upper fields. You need to choose what your sequence is going to be and as has already been said, add the shift fields filter to the shots that differ from your sequence.
I would recommend making a sequence in 10 bit uncompressed if your drives are fast enough and copy your edit sequence into that. All the DV shots then need to have a shift fields filter applied and all the other material has no shift field filter.
That should then play correctly. From there if you are playing out to digi beta then that is also upper as are PAL DVDs. The advantage of making the final sequence uncompressed 10 bit is also your titles and graphics will look much better than DV codec would allow. My golden rule for PAL is to avoid DV codec at all times.