KDE 4.4.17
KMAIL 4.14.10
Plasma 5: 5.5.4
QT 5.5.1
interface language Italian.
This is a default installation of Leap 42.1. As Kmail in the default with Leap
is held (rightly I would say) at version 4.14.10 this applies KDE 4 and Kmail
running on it. 
However in the thread I did open in opensuse-KDE mailinglist another user
complains that this is also true in TW for a pure plasma 5, framework 5, kmail5
installation with the very same symptoms. 

In my case:
First aspect: 

when opening the user A, and setting Kontact to automatic start up, and if you
put: check mail on start up, or if you click on check for mail right after the
program started, filter will fail. The mail will be retrieved, it will be all
put into the default folder of the respective account. 
If you select the folder and go into the menu and choose: folder: apply all
filters to that folders, then the mail is filtered and distributed correctly.
But, new mail will again not be filtered at all. This will apply to all
accounts present. 
Now, if you logout and login again of that user. Then the filers will work now,
no matter if you do respect the wait period or not. That is why I speak about a
race condition of something starting up and not being ready when requesting new
mail. 

Second problem: 

this issue is not without consequences on the filter listings. You will be
prompted sooner nor later (normally on every start-up by another filter) with a
window telling that for the filter X Kmail does not find the account. You are
asked to choose ... but the list is empty. Now, if you click on the first line
of the empty window you can actually change the grayed out status of the OK
button to normal. And press O.K. and for now you are done. 
In about 30% (estimated) of this events you loose the filter in question. It is
deleted of the filter lists and does not exist any more. 
If you click on cancel when this window appears you DO loose that filter
immediately. Sometimes two filer are hit, so two separate windows to confirm
pop up one after another. 
With the time you will loose at least half of all your filter. You may recreate
them, but still for unknown reasons some vanish, and some have this problem. 
I have noticed also a slight dependency on one specific settings: if you have
let us say about 6 mailboxes with pop with the same numbers of accounts, then,
if you set the filter to be applicable to that specific account and not to the
others, this filter will be hit much more frequently with this "cannot find
account of filter" dialogue. 
Once the "amnesia" started it will "cycle" through and loose one by one a
filter in the list (direction generally from top to bottom - without guarantee,
it sometime can hit in the middle of the list). In this cases you may not be
presented with the little window complaining not to find the account. You will
just loose the filters one by one.  

Now let us speak about the dependency of this with "waiting". If you start up
the user A with kmail in automatic and a) either open another user and then
return to kmail to check mail. Or b) you do wait at least about 40 seconds to 1
minute usually the filter never fails. But it fails always and repeatably
triggered by immediately asking for mail. Then the filter does not work and
will not work up to logout/in again as stated. 

As this bug is loosing data (filter setup with a lot of care) it is quite
annoying and may also ruin filter collections of users.