Andrea, if you are using EasyBD Lite, disable b-pyramid because it does not like it. This also helps compatibility, as does disabling weightp. You might also try closing gops.
Level 4.1 requires 4 slices, whereas Level 4.0 does not. Once you have chosen one, there is no reason to change when remuxing (as you said you did in post 2).
Does multiAVCHD not accept elementary streams as input? If it does, that's what I'd use. What are you using to encode?