You'll notice that it only happens when you gain both LS and DS points. Basically, net points means which side you got the most points on.
e.g. If you get 2 LS points, but 5 DS points, then the net amont of points will be DS because you'll have gained more DS than LS.
Hope that makes sense :D
Edit: Damn wasn't quick enough! Also reminded me though that unfortunately this net system doesn't work with influence. Say you gain influence with Kreia but lose it with her as well, then there is no net influence gained. I think they should add that in the patch!