After sometime work in background I get notification that mail is received but I can't see it...

I start eM Clint properly and I get all emails that I received during night. I can see body of all messages and I can read them. But, after sometime work in background I get notification that mail is received but I can’t see it. And message will be downloaded next time I go online. I fount stupid solution that I exit app and start it again and I can see message. It happens again after working in background for some time… And it is happening every day several times…
I set sync time for 5 mins.

If you disable conversations (Menu > View > Conversations) does the unread/new message display correctly?

The sync interval only applies to POP3 accounts, as well as contacts and calendar. If you are using IMAP or Exchange, it will not affect your messages.

If you go to Menu > Tools > Accounts and click on the IMAP tab for your account, you can select to download messages and content for offline use. Check that you have selected that and see if that makes any difference to the online issue.

I made changes, and I’ll monitor for few days. 
I’ll let you know if it helped!
Thanks for quick answer!