The Media Browser in both Premiere and Media Encoder doesn't like to display certain types of folders. The folders that I am having trouble with are folders that have been copied to my local drive from a Google Drive folder. These show up with a custom icon in Windows File Explorer. They don't show up at all in the Media Browser in Premiere or Media Encoder.

A fix that I have found is to set the custom icon back to a default icon in File Explorer but this is pretty painful if an entire project has been downloaded from Google Drive with many folders in it.

Right click on the folder
Choose "Properties"
Click on the "Customise" tab
Click on "Change Icon"
Click on "Restore Defaults"
Click on "OK"

The folder will now show up in the Media Browser after selecting “Refresh” from the palette menu.