Before you go further, note that ZCS supports IMAP "SEARCH HEADER" searches as of 5.0.5 (see Bug 7384 – IMAP search on non-indexed header returns error). Do you need something besides that?

Does it work if you remove the quotes around "is:unread"?

What problems were you having, and is there anything in the mailbox.log file?
Also, does restarting mysql help?

Looks like a SMTP transparency problem (RFC 2821, section 4.5.2). But nobody else has had this issue and we haven't changed either our SMTP client (JavaMail) or our LMTP server.Are you running anything else on your network that might be mishandling SMTP transparency? An antispam/antivirus box, a...

[quote user="bonoboslr"]My question is - where / how can you find the FolderId of the Inbox folder?? There is absolutely no documentation on this - neither is there any for the zmprov cds command so I am starting to pull my hair out.[/QUOTE]
The Inbox always has folder ID "2".

Messages are returned as-is, exactly as they were received from the MTA. No character encoding is done on them.

You could use the SyncRequest SOAP call to track changes via polling. You could also write an extension that registers listeners on the Mailbox objects. Neither requires altering Zimbra code.

Same commands as normal for fetching folders, only adding either -v for verbose or -d for debug. (Not sure which is the one you want -- try and see.)

That data is actually returned by the server. If zmmailbox isn't displaying it, you can still get at it by turning on debug/verbose mode and looking at the "s" attribute on the folder.

The tags are stored as IMAP keywords (i.e. as metadata, not in the message headers). Mutt should allow you to filter on IMAP keywords.