You sure that the original footage was shot interlaced? The information I found on the camera is that it shoots progressive.
Hard to generalize about what looks better – interlaced or progressive – except that interlaced can look pretty dodgy with computer play-back. Otherwise, much depends on the material that was shot.
Bear in mind that de-interlacing per se throws away half the information. Frame Controls tries to compensate for that loss. Going from Pro Res to h,264 is a major compression step by itself; adding more filters in our attempts to improve results also can increase the possibilities for errors. Maybe that's what happened here.