With which browser, which skin, which website does this happen?

Clicking the notification should take you to the actual message. Once that page with the message is loaded, the notification is marked as read.

Is that not happening?

In T112477#1635777, @Aklapper wrote:

With which browser, which skin, which website does this happen?

With Firefox on Vector, as tested in Fa WP (from which the screenshot was obtained).

In T112477#1635824, @Mooeypoo wrote:

Clicking the notification should take you to the actual message. Once that page with the message is loaded, the notification is marked as read.

Is that not happening?

It does take me to the page, but that does not result in the item getting marked as read or the counter being reduced by 1.

In T112477#1635889, @Huji wrote:

It does take me to the page, but that does not result in the item getting marked as read or the counter being reduced by 1.

Does the counter update correctly if you refresh the page?

Also, can you check if this is still happening? The new Echo layout will be redeployed to Wikipedias tomorrow.

In T112477#1668755, @Catrope wrote:

In T112477#1635889, @Huji wrote:

It does take me to the page, but that does not result in the item getting marked as read or the counter being reduced by 1.

Does the counter update correctly if you refresh the page?

Yes, a refresh fixes it.

Also, can you check if this is still happening? The new Echo layout will be redeployed to Wikipedias tomorrow.

It happens right now. I will check back tomorrow as well to see if it changes.

Tested again: now the yellow badge for new messages DOES disappear when you click on the item in the notification drop-down, but the counter still DOES NOT decrease by 1.

This is the same mechanism we use to auto-mark-as-read Flow messages when you visit the Flow board.

I cannot reproduce this issue. Here's what I do, let me know if I'm missing something:

1. User 1 creates a new Flow topic on User 2's talk page
2. User 2 logs in and sees
   
3. User 2 clicks on the 'messages' notification icon and clicks on the only unread notification
4. User 2's talk page is displayed and there is no more unread notifications
   

The steps are correct. Yet I did exactly that right now on Persian Wikipedia and I ended up with this (note that numbers are localized but you can tell there is 1 where it should be a zero):

In other words, its background changes from blue to grey but the number is still 1 until I refresh the page (or go to any other page for that matter).

edit-user-talk is not used for Flow. This task is regarding old-style talk:

https://git.wikimedia.org/blob/mediawiki%2Fextensions%2FEcho.git/1f7a3ceb83382e689cc82e4eb5b7e021a798f51a/includes%2FDiscussionParser.php#L60

Change 242123 had a related patch set uploaded (by Sbisson):
Add target-page to edit-user-talk to dismiss notification

https://gerrit.wikimedia.org/r/242123

Change 242123 merged by jenkins-bot:
Add target-page to edit-user-talk to dismiss notification

https://gerrit.wikimedia.org/r/242123

1. the issue is reproduced(the screencast is attached)
   fa_wiki_incorrect_update.mov7 MBDownload
   on https://fa.wikibooks.org/wiki/%D8%A8%D8%AD%D8%AB_%DA%A9%D8%A7%D8%B1%D8%A8%D8%B1:Zilant17#.D8.AE.D9.88.D8.B4_.D8.A2.D9.85.D8.AF.DB.8C.D8.AF

wikibooks posts 'Welcome new user' message on User talk page - other wikis do it differently: no reference to User talk page and the icon is different.

2. I checked the fix on http://fa.wikipedia.beta.wmflabs.org/w/index.php?title=%D8%A8%D8%AD%D8%AB_%DA%A9%D8%A7%D8%B1%D8%A8%D8%B1:Etonkovidova&gettingStartedReturn=true. The new user 'Welcome' message is the same style as in wikibooks (as in #1).

• a user clicks on Messages - the background turns grey
• a user clicks on the Welcome message - the Welcome message redirects to User talk page and the counter becomes 0.