Mac mail - mail showing up hours or days later

I've been having a few problems with my Mac Mail lately
using OS X 10.9.2
Mail v 7.2
1 - each morning I will read my new messages.  then an at various times of the day, new mail will come in but it will be dates hours or days ago.
2 - I'm having search issues.  I can't find emails in the sent folder that I sent an hour ago, or when I search for it, it wont show up in the search.
3 - read emails seem to be going into my archive box
4 - when I search for sent emails, it seems to find 10-20 of the same email (it looks as if it is saving it every few seconds since each email looks to be a progression of the full message i.e. first email jsut has the to: and subject linel next email has that plus 1-2 lines of text; next email has 3-4 lines of text, so an and so on thus the 15th email may be the entire email sent.

You're welcome.
So what is itunes doing when it syncs my mail? Just the settings? Is it even worth keeping the sync box checked in itunes then?
Account settings only, which is a one way transfer process only - from your computer to your iPhone. After account settings are successfully transferred from your computer to your iPhone via the iTunes sync process, there is no reason to keep this option selected for your iPhone sync preferences - unless you make a change to account settings on your computer that you want automatically transferred to your iPhone.
I suggest checking your account settings on your iPhone and use Never for removing messages from the server when downloaded for the account settings for each account. You can removed messages from the server in other ways. If you use the Mail.app on your Mac for accessing the accounts, you can removed messages from the server as needed with the Mail.app, or via webmail access for each account.

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