I'm definitely having this problem, but I don't know how to solve it, sorry, that's why I searched this question and landed here.
My problem is slightly different in that it seems determined to keep the Inbox the same size, so say I have 25 emails and get 3 more, if I delete the 3 new ones it will poll the inbox and say I have 3 new emails but when I go into it it's 3 old emails that have been picked up in order to fill the 3 empty spaces! Usually it is at least able to immediately identify them as old emails but not always, sometimes it loads up a bunch of emails as if they were received that morning at various times ranging from about 8.30 to 9.15. I don't want to delete them from my server as they are emails I want to keep, but don't want to leave them here at the top of my mail list because they are out of order, so have to keep switching my settings for deleted mail. I can't use the "archive" button cos it will not allow me to create a new folder to archive my mail into, I can only archive to existing folders - inbox, outbox, sent, drafts or trash.
Really hoping someone can help us both, I'm not sure I can even roll back to an older version because mine is newly installed directly to 3.503.
PS I am not married to K9 mail, I am happy to consider recommendations for other mail which will:
*Work with free hotmail (K9 allegedly doesn't but it does!) via POP
*Only notify of new mail ONCE, not like the native mail system which will tell you ever 5 minutes that you still have new mail.
*Allow bulk processing of "mark read"
*Covers the basics, i.e. it is reliable, sends, receives, doesn't randomly miss mail, is capable of leaving mail on the server and leaving it alone, does not automatically synchronise folders with the server.
I tried Maildroid and Shangmail and Yandex and I'm sure others I now forget but didn't like those.