Both apps are watching all three folders. Neither app is moving the messages to the delta chat folder.
Yes, other messages are appearing in the desktop app.
I retried it again this evening. This time the Autocrypt Setup Message appears in the desktop client. It actually appeared as a two part message in the desktop client. However, clicking on either one of them did nothing. The second part of the message has a download button I can click on, but that only offers to download an html file to my desktop computer. Clicking on either part of the message does NOT open up a window that allows me to enter a code.
(P.S.: It took almost 24 hours for the encryption message I sent last night to finally appear in the desktop app - the one I told you about in yesterday’s posting about how I was waiting for over 30 minutes for the message to appear in the desktop app.)
I have attached a screenshot of what the message in the desktop app looks like, it does NOT instruct me to click on the message as you suggested: