Is it pop3 or an imap account? It sounds like imap behavior. You should keep the autocheck time above 5 minutes, i usually recommend 8 - 10, because Outlook may not be finished checking for new mail before the next check starts as it is limited in how many threads it can open to a server at one time. If you have a lot of folders and new mail, it might need more time to check each folder.
You can check your send and receive settings to see if all of the folders are being checked or just the inbox. Use Ctrl+Alt+S to open the dialog or look on the Send & Receive ribbon > send/receive groups > configure send/receive.