Here is a image of 2 folders in DO 13. One truly empty the other not.
The lower one contains all this and more.
I"ve entered in and out of the directory several times thinking it would update but no such luck.
Here are the preference settings that might affect this...
Assuming you're already using 13.4 (if not, try that first), go into Everything and open its settings menu. In there is a button to make it rebuild its index. Try that.
While there, make sure it is configured to index the things specified here:
https://docs.dopus.com/doku.php?id=additional_functionality:everything_integration
