Why are my e-mails downloading as already read?

Have you checked your gmail settings under:

Settings > Forwarding and POP/IMAP > POP Download > 2. When messages are accessed with POP

One of the options here is to “Mark gmail’s copy as read”. Do you have that option selected?

No. It is set on “keep Gmail’s copy in the Inbox”. All of the mails downloaded to Gmail show ‘unread’ until I actually read them. And even so, since this is downloaded into Gmail as POP I don’t think it would affect the IMAP, would it?

That was my first thought, too – but I think it’s the only relevant thing in Gmail that could affect your setup. I would probably check your phone’s settings next, but I have no advice to offer there. :(

Could you have a filter that is too broad and catching all your email and setting it as read?

Change your password. ASAP.

^ Good idea. Didn’t think about that. Someone could already be reading the emails. Also, make sure you’re using 2-factor auth.

I’ve had several iPhones, it’s not a setting option to show mail as being already read, and the only time they show up as being read is when they have in fact already been read. Gmail has a setting you can access from a computer or a mobile browser to log you out of all other devices you may be connecting from, you need to do this before changing the password to prevent anyone getting your emails from seeing that you are changing the password (because they send a confirmation link). I recommend changing the password to the alternet email account you have on file (the one to retrieve a forgotten password), and any accounts set up with your email addresses since its very easy to get information for all of your accounts when they are linked together.

Good call, @cheebdragon.