I'm having the same problems with my godaddy.com POP email account.
The techs at godaddy INSIST this problem is with the most recent update/upgrade to El Capitan, but that was weeks ago and my email server stopped retrieving email yesterday at 102PM. Except sporadically. On my Macbook, NOT my desktop.
They have led me through these steps:
In order to setup your email in Mac Mail, please follow the following steps:
1. Mail
2. Add Account
3. Other Mail Account
4. Enter Name, Email Address, Password
5. Click Sign In
6. Applemail will show a message saying “Unable to verify account name and password”. This is normal
7. The window will show a very similar window but will add fields for Account Type and Incoming/Outgoing server.
8. fill in those fields with the settings found at http://emailsetup.secureserver.net then click Sign In to continue setup.
Which I have followed to the letter. Including moving all my email into a temporary folder, deleting the account and starting at the top.
What I get NOW when I run Mail Connection Doctor is: SMTP account connection and login to server succeeded, i CAN and HAVE been SENDING email OUT, but on the POP side I get: user and/or password not recognized.
I'm stumped.
I'll try calling Godaddy tech support ONE MORE TIME and then put in a call to apple. After reading through all these troubles people are having, is Apple actually taking responsibility for this or blaming all the other email providers? I have email. It's on my godaddy account. I can log into my workspace account to access them. My Verizon account is working. Just not my godaddy-linked email.
But nice to know I'm not the only one this is happening to.
Norm