i_do_it
So I just tested this (with v1.17 + PHP 8.1) by creating a ticket via email, responded as Agent which auto-assigned myself, replied back as the User to the reply the agent sent, the message was appended to the thread, and my Agent got the New Message Alert.
Not sure exactly what's going on in your case but I suspect that your User's email is being considered a Bounce or Auto-Reply. You can post the raw email headers here (censoring any sensitive info of course) from the email that didn't alert the Agent so we can review.
Also make sure your cron job is set to use the correct PHP version.
Cheers.