I've been experiencing this problem since... ever, with any Thunderbird version (at the moment I'm using 45.8.0), both Windows and Mac OS.
On all my IMAP accounts I use server-side filters (e.g. GMail labels).
When I open Thunderbird or I search for new messages, my subfolders unread emails count doesn't get updated. So, If I want to know if there are new emails inside a particular folder, I have to click on this folder: this way the unread message counter updates and, of course, I see new messages. Pretty uncomfortable.
If I use local (i.e. to the client, not server-side) filters, this problem doesn't happen.
I've searched the Internet a lot about this problem, but never found a solution. Any suggestion? Any hidden option to tweak?