Does this still occur?

You have to select folders once per session, in order to get the unread count for them.
Afterwards they refresh correctly.

This first step is a bit awkward, especially when having lot's of folders and sieve rules for distributing emails into folders.

I am in the same situation having a lot of folders and sieve rules distributing the emails. So perhaps it is possible to preconfigure the subscription of all folders in the .GNUstepDefaults or something like that.

See also http://www.sogo.nu/bugs/view.php?id=1289

This is a real problem for all who use Sieve to pre-sort their mails.

I propose the function to check all folders for new mail (instead of just the INBOX) should be implemented optionally (disabled by default), so anyone who enables it knows that he will generate more load on the IMAP server.

Fixed - see: http://mtn.inverse.ca/revision/diff/a4f6c377a41454eb21ed5b253cb7d07fc2c1a55e/with/3c7106a946b0d9786d46c4f0c0a7e5bc1e5f8684

We now check for new mails on all folders that have Sieve rules defined to move mails into.