There are 2 possible reasons for this:

1. The Folder does not have Child layers

All Folders must have child layers or Export Kit will stop the output. A Folder without child layers is considered empty!

Solution: (a) remove the folder, or (b) add child layers to the folder

2. Your Folder is Locked

A hidden feature of Export Kit is the ability to break the output on a specific folder by locking it.

We do this because in the past users requested a way of "preventing" the client from exporting the PSD until they were paid in full - this is the way.

Solution: unlock the folder