I'm also using Steadtler Lumocolors for lines and 
haven't had any trouble with fading when painting 
over them.
I'm using a brand of acrylics called Chromacryl. 

I'm not sure if I have understood correctly but it 
appears that your lines are affected as soon as 
you paint over them?
If that is the case, it does appear that the paint 
you are using is affecting the lines drawn.