Hi there Milivoj
I have exactly the same problem, same camera, using FCP 6. The L&T process turns the 50i clips into 25fps clips with No Field Dominance.
I have tried all possible variations of forcing the clips to take on different Field Dominances (Lower, Upper) and matching these with a variety of sequence settings but although I can make the programme look great in the canvas, as soon as I export to QuickTime the picture has horrible interlacing problems.
I have found another references to this problem but no fixes.
https://discussions.apple.com/thread/3554680?start=0&tstart=0