I have done unread tests again on all my 3 email accounts including Gmail & Live IMAP accounts with this time (mark messages read after x secs) “disabled” and and still cannot fault it.
Sounds like its definitely specific type of accounts that are the issue here like “office365/exchange” accounts which have this unread issue. Or possibly “some other program” installed affecting the unread count.
I see there is also another ticket below for Unread count issues as well which also mentions Office 365/Exchange.
Bug: Unread message count incorrect - Mail - eM Client
As per the other thread on this subject if you have eM Client Professional lodge a support request via - Support | Remote Assistance | License Manager | eM Client