Custom skins won't take
 

I have 8 109 E 4's in my coop but only 4 out of the 8 hold on to the custom skins. When I start the mission 4 still have the default skins on. How come?

Take a look into the Groupsetup in the FMB, you can assigne each single aircraft a different skin, if you like.

Just check all the planes individually if the skins are set correctly I would suggest for starters.