Just set up Mail.  It downloaded 5,000 emails...

I just downloaded Mountain Lion on my MacBook Air.  I am still new to MAC, I am in the process of transitioning over from PC, so still trying to figure out the basics. 
When I set up the Mail app, I added my hotmail, gmail, and yahoo accounts.  Now I have thousands of old emails, all showing as unread.  These are emails that I deleted years ago and do not show up on any of my PC's, my iPhone, or iPad.  I even signed in to a coworker's computer to see what would happen and the account was fine there.  One of my hotmail accounts has 22 emails in it on my PC and my phone - has over 400 now on this mail app.  I have my iPhone set up to delete from server when I delete on the phone - so I selected a new email on it, deleted it, then signed into the accoun on my PC.  It had been deleted there too.  It is still showing as new and unread on here.  What is going on?
I'm concerned too, because I just got a MiniMac, and don't want to have to go through it again when I set that one up.
A little help?
Thank you!
John

Thanks Joe - they are. Hotmail and Yahoo.  So, before that, should I take off the setting where it deletes from the server, so it doesn't wipe out my accounts in real life?
I just can't understand where they could have come from - some were deleted in like 2009.

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