MultiAVCHD will NOT output an interlaced file unless it is reporting the source as interlaced. There are no settings within MultiAVCHD to change a progressive source into an interlaced video unless you manually altered the detected settings.

You say you are 100% sure that you fed MultiAVCHD a progressive source. Well have you rechecked to see what MultiAVCHD reports the video as in the step i mentioned above? Because if it is reporting it as 1080p and not 1080i it is impossible for it to output an interlaced file.

Probably best to double check because your problem isn't down to MultiAVCHD. Replying with a cocky remark about "you're not that dumb" when someone is trying to help you really isn't the way to go especially when you haven't bothered to double check your source file in MultiAVCHD first. Sometimes it's easy to miss something and rechecking can rule out a source file problem.