We are working to this bug, we will release a new version which fix it. In the mean time you can use this work around (you need to do this each time you launch the app or you open a new window with in the app).

  1. Launch CleanText
  2. Hold down the “Option” key
  3. Click on the green light at the top-left of the Clean Text edit window.

All of Clean Text window now displays on the desktop.

Related Solutions:

What is the difference between Clean Text and Clean Text Menu?