Additional Asset Directories to Cook being Ignored!

Out of nowhere my packaging started to completely ignore my listed folders in “Additional Asset Directories to Cook”. My builds currently are missing about 100 MBs of content and will crash on load.

Does anyone have any idea what it could be?

To add: Even though I am specifically stating to include all files in a specific folder, they do not get put in and my package will result in 962+ "Warning “XXX” Imported “XXX” but it was never saved as an export.