I think I know the problem you are having, I was struggling with a simalar thing.

In mail if you look towards the top of the window, there are some Tabs, hide, Inbox, Sent etc.

If you click on inbox it will give you a choice of the accounts you have set up.

Click on one of them, and it will the show up on the left hand side under Inbox, along with your other accounts, separatley.

The same with sent.

Its not Ideal but is better than no separation.

Andy. P.S. If im way off what you are talking about, then I appologise, I just came across this thread when I was looking for a solution to my problem.

I had to go in Settings and turn off each account go back to Mail.

Exit Mail without doing anything and go back to Settings and turn each account back on.

This bug is a configuration issue where the programmer assumed the user would add accounts after the install.

Minor irritation, fix is to fool the system into thinking these are new accounts.

Picked up all of them and displayed the mailboxes correctly, so no, not necessarily a bug, but a glitch unique to your device, or an possible a quirk with the specific accountsproviders.

I have found the solution and its very easy.

Open up the Mail app 2.

Then select New Smart Mailbox 4.Click on the drop box that say Any Recipient and select Accounts 5.

Click on the the second dropbox menu and select which account you would like to use.

Gmail,Yahoo,Hotmail,etc.) 6.

Fix other settings accordingly and select OK 7.

Repeat steps until all accounts are in separate folders I hope this answered your questions.

I liked it better when they were separated and listed under my inbox, but at least now theyre separate.

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Seperate Inboxes In Outlook For Mac