If the upload input has a file but then the user decides to create a folder, the file is uploaded when the "Create Folder" button is clicked. Once the upload is complete, the folder is created but the file doesn't show up anywhere.
I verified this on the demo site with TinyMCE. On that note, it appears the ckEditor File Browser issue with Chrome is back. I think that issue, the last time we saw it, was caused by ckEditor though and not mojo.