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It's probably something in the POP implementation. Too bad GoDaddy charges extra for IMAP :/

That's because GoDaddy is a POS company that could care less about you, your websites, or your email.

Any company that is still forcing POP on it's users nowadays should be abandoned immediately.
 
Fix!!

I found another forum post on here regarding the same issues with IMAP, and the solution was to uncheck the option under mail preferences -> accounts -> advanced -> and UNCHECK "automatically detect and maintain account settings". I unchecked for all accounts, closed and reopened mail, and every email that has come in to these accounts since I installed Yosemite finally all downloaded. Hope it works for others as well.

It's worked in my POP accounts. Thanks!!!
 
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