I would suggest you control for the following:
in opensuse the Kmail/Kontact application is given with a preconfigured Agregator group considering linux, kde and opensuse activities. 
Once you have a mail, you are shown "1" in the counter, respectively more if you have more mail. Once you read them, the counter goes down. If all mails are read, by hierarchy, now you are shown the number of unread messages in the aggregtor app. So if there are 3 news, you are shown the number three. Once mail is available again, the number will show the number of mails. 
I am not aware if you can deactivate the monitoring of the aggregator app. But you can surely, if you do not use the aggregator, take of the groups. So the problem would vanish. 
If instead you should encounter that one of the mails is always "unread" although it had been opened, you may have run into a bug crashing kmail (and hanging the status of mails until a "akonadictl restart" in CLI and a closing of the "zombie" kmail via the syscontrol application. 
This bug mentioned is known and reported. 
So you will have to live with it until the new version of kmail that should arrive with 15.1. 
Else this would then not be a bug but a feature (no pun intended) and somebody more educated may enlighten you about the possibility to change this (wanted) behavior. 
Kind regards.

And while reading that this is probably the latter case:
bare in mind that if you use spamassasin, clamav (especially) and also a lot of filters, there may be a considerable time span (several minutes until half an hour) until all the filters are through and the messages are correctly attributed, thus in the meanwhile they may be listed as arrived but are not visible because not attributed to the right folder. 

I do not know if this could be your case. Just a guess.

thanks

i use spamassassin and 3 other filters to route to different boxes.

if i manually apply all filters then it takes 3 or 4 s. for 3 messages.

i don't think this is a filter problem.

>> So you will have to live with it until the new version of kmail that should 
>> arrive with 15.1. 

15.1 for what software ?

i know kde apps 19.12.1 , kmail 5.13.1 but 15.1 ...

(In reply to Philippe ROUBACH from comment #3)
> thanks
> 
> i use spamassassin and 3 other filters to route to different boxes.
> 
> if i manually apply all filters then it takes 3 or 4 s. for 3 messages.
> 
> i don't think this is a filter problem.
> 
> >> So you will have to live with it until the new version of kmail that should 
> >> arrive with 15.1. 
> 
> 15.1 for what software ?
> 
> i know kde apps 19.12.1 , kmail 5.13.1 but 15.1 ...

My bad sorry, I meant the 15.2 version of Leap. I think currently you are maybe using the KDE repos with the 15.1? 
Supposing you are using mariadb (as opposed to postfix that some do) did you check if (after this happens and you simply exit kmail) there is a non reactive instance of kmail staying resident once you exited via the menu bar? 
When I encounter here the problem, if you exit and reenter without manually terminating it, I have kmail segfaulting, this whether I restart akonadi or not. If instead I terminate it manually and restart thereafter, then the mails are correctly shown. 
I think the very same problem is present in the kmail 5.10.3 Version of the main repo (KDE Frameworks 5.55). 
You never get any segfault / backtrace?

As indicated in "description" I get last version of:

plasma : 5.17.5
frameworks 5.66.0
kde apps 19.12.1

with the last kmail 5.13.1 I get only one time a crash when launching kontact. since no more.

fir severa

I was able today to reproduce the issue on the "base installation" of kmail, from Leap 15.1 that is:
Plasma 5.12.8
Frameworks 5.55.0
QT 5.9.7
As filters I use spamassassin and clamav. 
Now, the issue was that two messages arrived on the same postbox with a certain lag of time. (About 1 h of difference). 
The first was visible, the second not. 
Issues encountered: the message that was visible would not shift to "read" status even if selected long time in preview (against the settings) and shifted only when double clicked and read (note: only after applying the workaround mentioned hereafter). The second message was not visible and stayed
invisible. 
I found however a workaround that you may try and that avoids to restart every time the program. Worked for me, that does of course not mean it will work for you. But if, it it would be nice if you report back: 
You have in the main view of kmail/kontact a "search bar". Here you can select to show you only new or also only unread messages. When selecting: show only new messages:
First I was now able to shift the message status of the message visible. 
Once "read" this one, the other one "reappeared". It was then possible to read the message normally and the status changed correctly. 

Regards.

ok thanks i will try next time it occurs.

kde apps 20.12.1
kde plasma 5.20.5
kde frameworks 5.78.0
qt 5.15.2

problem still there

kde apps 20.12.1
kde plasma 5.20.5
kde frameworks 5.78.0
qt 5.15.2

problem still there