Apple Mail - Amber color sometimes in Mailbox Pane in Yosemite

Hi
I am running OX X Yosemite 10.10 and using Apple Mail. Sometimes in the Mailbox pane on the left I see the top of the column glow amber and fade down the upper part of the column. It almost appears as if the color is moving. Has anyone else seen this and if so do you know what it signifies? My guess it means it is checking mail, but it does not to it consistently to affirm my guess.
Any help is appreciated!
Brandon

solved it without delete/add back (which would have been a pain)
turns out the having INBOX in the mail app path prefix setting (mail/ preferences/accounts/advance) was causing the entire account to not show up in the mailbox pane.
I have other email acts where it works only with INBOX in this setting. Still haven't figure out what makes this necessary sometimes, and not other times. Once the account showed up in the bottom of the mail pane, I was able to expand it and highlight the individual mailboxes that appeared (sent, drafts, etc), and then select the "Use this mailbox as" command which is at the bottom of the Mailbox menu.
Seems to me that different IMAP servers present themselves to mail clients with a fair amount of variation, so setting up Apple's mail app for one IMAP acct may be quite different from another.
I wish I could find a really good tutorial which thoroughly explains mailboxes in the apple mail client and mailboxes in an IMAP server and how they all interact, but anyway, its working ok now.

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