Some mails never come in the box "inbox" and appear only in "all mails"

That’s the title of an old problem!! And that problem always exist! Impossible, looking in the support, to find a pertinent answer or, better, a solution!!
On a fresh install of the last release of eM with a new gmail account … I have that problem. No rules at Gmail level, no rules at eM level … nothing specific.
It’s boring!! And nobody in eM support seems to consider that it’s a real problem.
Some saids it’s Gmail fault but :
    it happens with other email providers (I saw that in eM support)
    if it’s gmail fault why other softwares (Courrier, outlook, thunderbird …) do not meet that difficulty?

Please find a solution!!

As far as I know GMail is the only provider who has a All Mail folder, and I am sure that eM Client Inc. does consider their implementation of GMail in the application to have some problems. If you have a Pro License, please open a support ticket with them to get feedback on what is being done to fix it.

If this occurs with some other providers, it is a very different issue. Recently there was one similar case with a Charter server, but this is not the same thing. It is just the way that particular server is setup, so it does not work with the type of IMAP that eM Client uses. A solution in that case is to use POP3. But most email clients work differently, so where a particular server is a problem in one, it may not be in another.

I researched this issue yesterday, and found this thread, along with a whole lot from some time ago, as this has been happening to me with my 2 addresses for some time.

As there has been no response from eM Client that has fixed this issue (all they keep saying is to disable or alter the rules), but when I had no rules to attend to, it had to be something else.

So yesterday I bit the bullet and deleted my accounts, and then eM Client. After reinstalling  it again the issue resolved itself, so obviously IMHO the issue is with something in eM Clients software. Reinstalling was no big deal, as all my stuff repopulated again from gmail. Problem fixed for now!