I have 2 IMAP accounts @Sky.Com (Yahoo Mail). Emails from either are appearing in both accounts. They are not being separated into the correct accounts.
Seems you have setup the same account twice.
Check which one’s Inbox in eM Client doesn’t match the Inbox in webmail and remove that account. Then add it back again and make sure when you enter the credentials in the web browser part of the setup, that you enter the credentials for the correct account. If you enter the ones for the other account, it will sync with that mailbox instead.