Well, for now you should probably verify that the new FEditor can actually insert animations to slot 0x0100. After that you can figure out why NM1 is weird. Worst case you just use NM2 for animations and NM1 for everything else.
EDIT: Confirmed working, inserted promoted Eirika animation into slot 0x100 and replaced her normal battle animation successfully.
You don't even need a new Nightmare Module, I just used 0x00 for animation played and 0x01 for the "separator".