I’ve been using Manjaro KDE for over two years now, and it’s always been like this: the Pamac icon in the system tray, which turns red to indicate available updates, doesn’t automatically revert to its original state after updates are performed. It doesn’t matter whether I perform the updates in the console (using Pacman) or directly in Pamac; the only solution is always to refresh the Pamac database. While I hardly ever use Pamac for updates, the problem persists. Has no one else noticed this before, or is there some kind of evil spirit lurking in my computer, trying to drive me crazy?
Yes, this is well known.
Of course, and it has been reported many times already — which you would have known if you had looked around the forum more closely. 
But it’s not a bug; it’s a feature — it’s how the pamac update notifier works. If you don’t like this, then you can try octopi instead. It also does not know that you’ve updated the system if you did it from the command line, but if you do update via octopi itself, then it will revert to a green icon instead.
Of course, octopi does not cover FlatPaks or Snaps, which pamac does do. So it’s a matter of preference.
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While not 100% perfect my install almost always clears the icon after updating with the pamac gui. Flatpacks seem to be slow to clear, but official and AUR are quick. Usually as soon as I close the gui.
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If it works that way for you, it’s obviously a bug and not a feature. As a feature, it would be completely ridiculous…
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Updates often need system restart to load updated packages.
If system is not restarted, Pamac update notifier (pamac-tray-icon-plasma on KDE) might not reflect that system is up to date immediately.
$ grep -B1 'Refresh' /etc/pamac.conf
## How often to check for updates, value in hours (0 to disable):
RefreshPeriod = 6
How To Ask Questions The Smart Way - Eric Steven Raymond
Don’t rush to claim that you have found a bug
When you are having problems with a piece of software, don’t claim you have found a bug unless you are very, very sure of your ground. Hint: unless you can provide a source-code patch that fixes the problem, or a regression test against a previous version that demonstrates incorrect behavior, you are probably not sure enough. This applies to webpages and documentation, too; if you have found a documentation “bug”, you should supply replacement text and which pages it should go on.
Remember, there are many other users that are not experiencing your problem. Otherwise you would have learned about it while reading the documentation and searching the Web (you did do that before complaining, didn’t you?). This means that very probably it is you who are doing something wrong, not the software.
The people who wrote the software work very hard to make it work as well as possible. If you claim you have found a bug, you’ll be impugning their competence, which may offend some of them even if you are correct. It’s especially undiplomatic to yell “bug” in the Subject line.
When asking your question, it is best to write as though you assume you are doing something wrong, even if you are privately pretty sure you have found an actual bug. If there really is a bug, you will hear about it in the answer. Play it so the maintainers will want to apologize to you if the bug is real, rather than so that you will owe them an apology if you have messed up.
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Then I suggest you disable update nagging, rely on the occasional notification on the forum.
I have heard about it - so don’t expect any weird network activity when you are asleep.
The nagging part of pamac - the tray icon - is akin to checkupdates from pacman-contrib.
checkupdates does not use the system metadata but a temporary downloaded set of data; the reason for this is simple; if it downloaded new system metadata it could easily cause a partially synced system; a partially synced system may exhibit stranger behaviour than that of a tray icon.
I don’t know exactly how the tray icon works but it is quite possible it works the same way.
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To check repository and AUR packages are up to date:
pamac checkupdates --aur
A little known forum feature is the ability to add .rss to the end of a URL and add it to your favourite feed reader application.
Example: this URL;
https://forum.manjaro.org/c/announcements/stable-updates/12.rss
when added will keep you updated each time there is a Stable Update announcement published.
Try it. 
Regards.
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I have not used pacman to update in quite some time so I do not know if the icon works as expected.I do know using pamac upgrade in the terminal the icon works as expected with KDE unstable and the latest Gnome stable.
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I’ll also recommend adding Stable Updates - Manjaro Linux Forum to your “Watching” list, being a regular Forum user. It’s how I’m usually first made aware of new updates being available; I don’t tend to bother with the notifier icon.
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What does all this have to do with this obvious bug that they’re trying to sell as a feature? I have NEVER relied on any notifier. That makes this red thing even more annoying.
I don’t actually think of it as a “bug”; just that the notifier doesn’t “automagically” detect an update having been performed and refresh itself … more like a “missing feature”.
That update notifier is related to pamac — note: not pacman — and it periodically checks for updates by polling the mirrors.
However, the icon is a separate process and does not know what you are doing with the pamac proper GUI package manager — unlike the octopi notifier, which is part of octopi itself.
Therefore, updating your system via the pamac GUI does not change the status of the notifier icon. If it does, then that’s just a coincidence with the timing by which the notifier polls the servers.
However, if you log out and back in — or if you reboot, which you should always do after a system update — then the notifier will poll for updates again on login, and will then see that there is nothing to update anymore, and it’ll turn green.
It’s either that, or right-clicking the notifier icon and manually telling it to check for updates again.
Is it clear now? 
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There’s already an upstream issue. Let’s keep the discussion constructive, please. Pamac is maintained by one person. Please show respect and have patience.
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Thanks @Yochanan, at least that’s a constructive answer and not just silly talk about features and so on. Of course, I have respect for Pamac’s maintainer, no question about it. It just annoys me that people are treated so disrespectfully in discussions about it. Thank you to the developers involved for their many years of good work.
Just to mention, I took the “feature” reference to be rather tongue-in-cheek – as it was doubtless intended – it’s unfortunate that subtleties in humour don’t always translate well for everyone.
That is all.
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I feel the same way about my native language. In many cases, it is much more nuanced than English, but this often gets lost in translation or even comes across incorrectly. The price of globalization …
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