Since Moodle 3.2 we aren't able to configure popup (Web) for instant messages. If I go to Message preferences I only see "Mobile" and "Email" (see attached screenshot). Since the configuration field is a string with the list of processors enabled, changing ANY of the values in that screen will disable popups for instant messages, and there's no way to enable it again.

Also, we noticed that messages are only marked as unread if the popup processor is enabled for messages by the receiving user. We think that the Mobile (airnotifier) processor should also do this, since the app can tell Moodle when a message is read. This can be done using the message_working database table like popup does.

Could be related:

https://moodle.org/mod/forum/discuss.php?d=345551