Hello Magma!
here I have new issue. The "factory circuit connector" , maybe the outside one, merges both red and green to one combined signal. Look at pictures:
1. outside building: http://i.imgur.com/IUxlKUG.png
2. inside building: http://i.imgur.com/MbjGYWU.png

in second image you can see, the chest have separated items. but look at the ouput signal... both signals are added.

Yes, that's because the yellow output entity is a constant combinator that sets its signal based on the signals the purple input entity receives. Unfortunately there's no way for an entity to send different signals to different networks. You'll have to use two circuit signal connections instead of one, or encode some signals to different channels.