It did it again!!! In the properties in multiAVCHD it definitely says
Video: V_Mpeg2
Resolution: 1920x1080p
and it says Scan type: progressive in MediaInfo in Media Player Classic and then the encoded m2ts file is still 1080i and in MediaInfo in MPC it says Scan type: MBAFF. Now tell me what I'm doing wrong, because I'm getting desperate, I did it exactly the same way with Jedi and it worked OK.