Has anyone seen problems with Apple Mail and POP?

Yes. And I know others.

I have to read Mail on my phone and wait for Mail on OS X to catch up when it feels like it.

Maybe the public forums are saying the same thing.

Yes - Godaddy POP accounts recently became erratic and then totally unusable; could send mail, but not receive it. Godaddy's so-called tech support's definitive solution: it's Apple's fault, just reset your password within the Godaddy web maint tool, and if that doesn't work, it's still Apple's fault; now go away. Of course, that was total BS nonsense. What seems to have worked is, for the Godaddy mail accounts, go to the 'advanced' tab in the account panel in Apple mail, un-check 'Automatically detect and maintain account settings'. Keep port 995 and keep Use SSL. No idea why it works, but all the Godaddy POP mail accounts here ( unfortunately a bunch ) now work.

It's obviously Apple Mail's problem; I have no issues with Thunderbird or Win 10 clients. GoDaddy just blames the victim and uses the support call as an upselling opportunity to get me to switch to IMAP at 5 times the price.

I tried your suggestion, but it still didn't work. What do you have for your "user name"? Is it set to your GoDaddy account name, or your email address?

Weirdly enough, inbound SSL was marked as off when I displayed the "account summary", despite the fact that the account settings were 995/SSL enabled. Resetting back to on didn't seem to help, though.

That suggestion did cure my godaddy problems. For user name I have my email address (not the email that godaddy uses to contact me nor my account name).

Here's a new wrinkle: Via "account info", I can see the messages on the POP Server. Apple Mail just doesn't want to fetch them.

Same issue. Problem started with update to 10.11.1 and contiued with 10.11.2 Beta. Latest Beta 3 now causes Mail and Preview to crash after a few minutes. Pop accounts work as confirmed by others on iPad and iPhone and any other OS X Mail application, such as Thunderbird and Postbox.

Definitely as Apple Maill issue 😢

I've finally managed to get the account working, though I'm not sure how and exactly which of my steps solved it. But my previous comment seems to have been a hint. The key to the workaround seems to be that you should ensure that the SSL displays as "on" in the Account Info>>Summary tab, which conflicted with the Account Preferences>Advanced> port 995/ "Use SSL" checkbox. I also cleared the "Automatically detect and maintain account settings" checkbox as suggested above.

Am also seeing problems with my AOL IMAP accounts. I continually get "login failures" that can't be repaired by re-entering the correct password. I have two accounts set up.