Obviously you have a non standard folder layout in your IMAP server.
System folders (Drafts, Trash, Sent) are normally beside the Inbox folder, not within it.

Perhaps you could change this behaviour by configuring your IMAP server differently?

We've at one point migrated from courier-imap to dovecot, and kept the single "INBOX." namespace we used with courier. I see now that the dovecot wiki suggest making the INBOX. namespace a compatibility name, and have a blank namespace in addition. Ref: http://wiki2.dovecot.org/Namespaces

But.. our GNUstepdefaults has:

    <key>SOGoSentFolderName</key>
    <string>INBOX.Sent</string>
    <key>SOGoTrashFolderName</key>
    <string>INBOX.Trash</string>
    <key>SOGoDraftsFolderName</key>
    <string>INBOX.Drafts</string>

so shouldn't sogo be using the folders within the INBOX ?

Not sure how hard it will be for us to switch to the blank + compatibility namespaces...

Actually SOGo seems to be understanding these GNUstepdefaults settings when it creates the Sent/Drafts/Trash folders (since it's creating them as INBOX.Sent/Trash/Drafts), but it's the webui that doesn't understand that these are what they are before we manually tell it.

Are you using a '.' as the imap hierarchy separator?

If that's the case NGImap4ConnectionStringSeparator should be set to "."
Otherwise strange situations like this can happen.

Yes, "." is the imap hierarchy separator, both on the dovecot side and specified in NGImap4ConnectionStringSeparator.

<key>NGImap4ConnectionStringSeparator</key>
<string>.</string>

Dovecot:

namespace {
inbox = yes
location =
prefix = INBOX.
type = private
separator = .
}

This is a bit counter-intuitive, but even if the IMAP server uses a '.' as a hierarchy separator, you have to use a '/' in the SOGo*FolderName settings.

I documented this in the last release docs since it is a bit awkward:

SOGoSentFolderName:

Parameter used to set the IMAP folder name used to store sent messages.
Defaults to “Sent” when unset.
Use a “/” as a hierarchy separator if referring to an IMAP subfolder.
For example : INBOX/Sent

Great, thank you! Now it looks much better :-)