Help with containers

Sorry Im a bit confused by what your diagrams are showing and a bit rusty, but think the problem might be that you have containers with defined but empty figures.

At any point in time, the container at the bottom, wins, anything defined in this container will overide the same parameters from the containers above. Likewise anything defined in the middle container will overide anything defined above, but be overridden by the same parameter being defined in a lower figure. However containers can have an instrument with no figure defined, in which case if that figure is defined higher up, that 'wins' and will play (effectively inherited from the parent container).

You seem to have figures defined that are empty, so they win over anything defined higher up. Just delete all figures in the woodwind container that arent woodwind, all figures from the brass that arent brass, etc. By delete I do not mean delete the 'notes' but select the figure on the parameter list on the right and delete it there, otherwise you will have a defined figure with no notes which isnt the same as no figure.

Lastly, you can define span, rythem, volume changes etc which can affect the above, but you havent got any of that (at least I dont think you have)

The containers are working from left to right and from top to bottom... the topcontainer is the (bottom)container in your screen
The topcontainer content is first executed.

Is  menu entrance "paramaterexplanations"helpful ? 

In your test.cognac the Archi container is the topcontainer
 

Note: try out some containers filled with chords progressions on top of instrument containers and with this parameter : harmony you will notice that the top harmony container is dictating
Replace it with a another chord container on top

There is a rootcontainer at the bottom as start filled with instruments for the arrangement and by adding containers on top of the rootcontainer you compose.(and with command :pack )..you put the instruments from the rootcontainer into a container where you for example it can divide (not possible in the rootcontainer )
Suppose you do have a rootcontainer filled with instrumenttracks and one is a piano : make a "snapshot" from the figure in the timeline ( bar) and add this figure ( for changing the piano pattern ) in a container on top of the rootcontainer (or pack )   

I guess I didnt explain myself very well lol and sorry. If you look at your brass picture, you have highlighted the middle container called strings and its instrument WW Stacc. WW Stacc has a figure defined (the bright blue square against the figure parameter label). That means strings contains a figure definition for WW Stacc that overides any in Woodwinds and it is empty so you will get no woodwinds playing whilst the strings container is below woodwinds. You probably have something similar for the No Brass container but it isnt possible to tell from the picture.

If you look at the woodwinds container, and click on Brass Stacc or Strings trem you will see the little box next to the figure parameter label is dimmed, which means the figure for those instruments comes from a different container, which is why you can see their greyed out notes.

You can click on the bright blue boxes where you have empty figures and delete the parameter.

Sorry I cant check your cog file as I am not near my studio, otherwise I'd send you back an example, but Ive attached a modified brass.jpg which hopefully highlights the problem.