Hi! I am not sure this is your problem, but I notice multiple puppets in your project and you mention "importing" the puppet multiple times. So I just wanted to make sure you understood how Ch gets updates to puppet artwork.
To start a puppet for the first time, you import the artwork file (PSD/AI) into CH. This creates a Puppet in the project panel. After that you should never import the artwork again in that way. Instead you keep editing the artwork and just save it. When you return to the CH window it will detect the artwork file has changed and refresh the existing puppet. If you are uncertain which file a puppet is now using, you can use "Edit Original" (CNTRL-E) and it will bring up the editor on the file Ch is using. That way you can be sure which one is the right file. (The puppet has a "Path" property that points to the artwork file.)
If you import the artwork multiple times, you will start a new puppet each time, losing the rigging you started from the previous puppet. I noticed multiple puppets in the project panel so was not sure if they were just different penguins or you were importing the artwork multiple times creating new puppets each time.
What I normally do is do File/Save in Illustrator/Photoshop, wait one second, then flip the window to Character Animator. You should see a popup come up saying is "processing". This is it loading the new artwork file. After that finishes, then keep using CH.
If that does not work, there is a "Refresh" button at the bottom of the Scene panel. Try clicking it then using ALT+Click on it. This empties some caches. Very occasionally something gets confused in CH and that clears the problem out. I don't think that is your problem in this case, but certainly the Body hierarchy in your puppet should be showing all the sublayers. The only time it hides them is if you dont give them names
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