Last week I had to build a watchfolder that converts an interlaced input movie to an H264 proxy using FFmbc. It took me quite some time to figure out that if you scale an interlaced video (with the scale filter) it automatically gets converted to progressive in this step. However as I further had to deinterlace it (with the yadif filter) this caused me some problems. This Google Search revealed a lot of useful information.
ffmbc -i Interlaced_Input.mov -vcodec libx264 -acodec aac -strict experimental -b 5120k -vf "yadif,scale=720:576" -y H264_Output.mp4