I have had the same problem with my progressive GoPro footage, when I converted it from the codec H264 to Apple Pro Res 422 HQ on Mpeg Streamclip, Final Cut Pro says the footage is interlaced. I made sure the boxes for interlaced footage were deselected. The only solution I have found is to use Compressor 2 and convert all the footage to Apple Pro Res 422 HQ and set the field dominance to progressive. I loaded one clip into FCP 7 to test it and the field dominance was none meaning it is progressive footage.