I have an email account with a directory structure that has Inbox as the parent, and many folders below that (as children). When server-side subscriptions feature is enabled, the mail in the Inbox parent folder is not displayed.

Reproducible: Always

Steps to Reproduce:
1. Setup an IMAP email account that contains a directory structure as follows. The names of the folders probably aren't important, but the fact that (e.g.) the trash folder is a sub-directory of the Inbox folder, is probably important. Note that email exists in the Inbox, as well as the sub-directories.

* Inbox
    * old-messages
    * trash
    * myspecialmessages
    * archive

2. Enable server-side subscriptions.
3. Allow the account to fetch the email from the server.

Actual Results:  
The trash and old-messages folders contain email. The Inbox parent folder does not display any email in the message list.

Expected Results:  
The email located in the Inbox should be displayed in the message list.

I've had this problem for many years, actually. It doesn't happen with Gmail, but it always happens with my Dreamhost hosted account. It always takes me a couple frustrating days before I remember what the problem is.

This might be another bug, but I also have trouble setting the Trash folder for the account. Even after disabling the server-side subscriptions feature,  it seems to mess up something fundamental to the account. When setting a Trash folder, it never keeps the setting and refuses to allow me to delete email. I have to delete the whole account and start again without server-side subscriptions.