Strange behavior, I created a test site with a home page and a gallery page with 2 shutter stacks in 2 separate containers. The 2 on the home page create the batch folder and the name of the images folder fine, but the 2 shutter stacks on the Gallery page do not create their subfolders? I am using Foundry 3 and the control center is a partial added to the second page (with Foundry 3 theme). website is https://cwdesign.space.
Share your project file with us so we can see how you’ve configured it. Point us to the page that works and the page the doesn’t work.
Create a ZIP file containing your project file. This is the file you open in RapidWeaver to edit your site. After creating the ZIP file, upload it using a service like Dropbox, WeTransfer, Droplr, or a similar service to create download link for us. Paste that download link in your reply.
working page (Home) = https://cwdesign.space
non-working page (Gallery) = Gallery | My Website
2 Gallery stacks on each page, in batch mode.
These folders were auto generated:
batch/ranch
batch/best
The other two were not.
Did you look in the Gallery page’s folder on your site? When I uploaded your project, and then visited the Gallery page, the correct folders were generated:
Ok, I understand now. It builds the structure under the page vs everything under one batch directory. It is working as designed - thanks for the assistance!
Correct. 
This is to help and try to protect against folders that might be named the same thing all getting dumped into the same location and overwriting things.