I'm using FastMail with mutt, though I'm not using macros to save messages. I'm not sure 
what your other config looks like, so I'm not sure how useful this will be to you. I'll 
post below my FastMail-specific muttrc settings for reference, but I'm just using the 
default "s" keybinding to (optionally tag and) save to Archive or elsewhere. 
Works on my machine, as they say...

        set folder = imaps://$my_usern...@mail.messagingengine.com:993/
        set spoolfile = 
imaps://$my_username:$my_p...@mail.messagingengine.com:993/INBOX
        set postponed = "=INBOX.Drafts"
        set record = "=INBOX.Sent"
        mailboxes =INBOX

Hope that helps.
JM

On Wed, Sep 02, 2015 at 08:19:12AM -0400, Matthew Phillips wrote:
I have a FastMail account and have set up a macro to send messages to
the Archive:

macro index,pager y "<save-message>Archive<enter><enter>" "Archive"

However when I do this and then check in the webmail they are not in the
Archive (and not in the Inbox).  Where are they going?

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