Version:           1.9.9 (using KDE 3.5.9)
Installed from:    SuSE RPMs

Each time KMail checks for emails on my online IMAP account, the selected message in the message list jumps to the last message received before KMail was started.
E.g., if there were 300 mails in the inbox before starting KMail, you start KMail and there may be, say, five new messages. Now you select the last, i.e. number 305. While reading it in the message pane below the message list, KMail checks again for new emails, and the selected message jumps back to number 300 while you were still reading number 305!
That's very annoying and leads me to restarting KMail nearly each time I want to read a larger number of new emails.

IIRC, I have been observing this phenomenon since KDE 3.5.7. I am using filters on this IMAP account.