Use H.264 or H.264-BR for export.
It's been my observation that the H.264 options all turn progressive, no matter what you have it set for.
But the H.264 Blu-ray options will keep it interlaced if you set it that way.
Thanks for your advice. When I put H.264 Blue-ray in I get Multiplexer. Should I leave this setting? I seem to be sending audio only when I ftp.
If you're making a real Blu-ray, you normally want separate files, so multiplexing would be off.
For computer playback, you can turn it on so you get one file with video and audio.