Your problem has a simple solution 
LPub expect the main model (complete assembly) to be the first in mpd order. You can change that in MLCad, Multipart menu > model sequence, select main model and press "up" till it's on top.
Otherwise... interesting project
LPub expect the main model (complete assembly) to be the first in mpd order. You can change that in MLCad, Multipart menu > model sequence, select main model and press "up" till it's on top.
Otherwise... interesting project