Thank you for the input.
You are absolutely right about the 720-example. 1080 is what we use almost all of the time, and sometimes the cameras are set to record to 1080i. When that hapens, the project will default to 1080i. That is what creates this problem.
The compressor i am using is Compressor v 4.3.2. I asume you have the same options if you want to export directly from Final Cut X. I have set up the profile in Compressor, and made it selectable from the share menu in Final Cut Pro X. I have checked extencively and would expect a field order, or deinterlace, option when setting up h.264 with mp4 wraper. I could not find one. If you find one, please let us know.
I asume that the rest of your post is correct, and it might be the reason why earlier versions of Compressor/Final Cut didnt even give you the option, and always exported to 1080p. For the current version that is not the case, creating a problem.