Same here but weird. I have 4 POP accounts set up and no iCloud email, gmail, yahoo, etc... They are all my own domain POP accounts.
At first, it said 11,000 unread emails in my "All Inboxes" box. Selected ALL and mark as "read". It cleared most of them out, but one account still remains with 4,000 unread emails. All of the accounts are hosted by godaddy, and they are all set up using the same settings, but for some reason, it is still seeing the one account as all unread.
Interesting development though... Here is what my account list looks like when I go to email app:
All Inboxes 4,053
Email A 4,053
Email B
Email C
Email D
Email A will not clear unread emails. I deactivated Email A, and then I got...
All Inboxes 2,341
Email B 2,341
Email C
Email D
And now Email B won't clear. I re-activated Email A after a hard restart, and now I have...
All Inboxes 4,053
Email A 4,053
Email B
Email C
Email D
AGAIN! Email A won't clear but Email B is now clear again. It appears that the first email box in the hierarchy is the one that will not clear unread messages. WEIRD!
Obviously a bug that needs to be worked out and no solution because of settings. Hopefully bug guys read this and get it sorted out.
Another question - it didn't download ALL of these emails to my phone did it?? Thats the most important! Had it originally set to 100 most recent emails per account.