Why are new unread messages marked as read?

Question

These problems popped up out of the blue last week. Nothing has changed in the Mail settings. I've worked with my ISP to isolate the problem as a Mac problem, not an ISP issue.
1. The new messages downloaded into Mail are not marked as unread, even if they they've never been opened or previewed. An occasional email will mark as unread. However, even if 5-10 new emails are downloaded at a time, they will usually all be identified as read.
The unread count doesn't change, even when new unread messages are downloaded.
2. At the same time that the issue popped up with the unread emails, a new Mail issue started. When Mail checks for updates it often shows that a new email is being downloaded and gives the audio alert for a new mail, but nothing has actually downloaded. I've checked my filters, trash and web mail to confirm that no new emails exist.
What I've tried:
1. There are no software updates.
2. Worked with ISP to identify the issue as being a Mail issue. Settings are all appropriate.
3. Disabled Mail account, shut down Mail, shut down Mac, restarted Mac, enabled Mail. Problem continues.

Answer 1

This might be way off base because I do not have a really good understanding of email systems, but look at these:
1. When you Sync your iPhone, under the "Info" tab in iTunes, do you have it set to sync your email settings? If this is not checked, your iPhone and computer Mail settings could be different and Mail could think you read a message on your iPhone when you haven't.
2. In Settings in your iPhone, go to Mail, Contacts, Calendars>Your Account>Account Info>make sure everything is correct here and then>Advanced> check incoming settings and see if there is anything in IMAP Path Prefix. I think this should be blank for your POP account.
Also, since this is a POP account, by definition, if you have read a message, shouldn't it be excluded from your Inbox? I'm guessing there is a IMAP vs POP conflict somewhere.