Unread mail count/indicator no longer working with filtered messages

I have a university Exchange mail account and I use filter rules to automatically move new messages to a number of mailboxes. These messages are are not "on my Mac" but they stay on the mail server (accessed via IMAP).

Since upgrading to High Sierra (I think), the "new messages" count in the dock no longer shows messages that have been filtered to one of these mailboxes. This is rather annoying because I keep missing important mail - I only find it once I scroll down my list of mailboxes.

I haven't been able to fix this - and I would welcome input on whether (and if yes, how) this can be solved with a simple change in my configuration, or whether this is something that Apple would need to fix.

Thanks!

Sebastian