Version: (using KDE 4.3.3) OS: Linux Installed from: Ubuntu Packages If a thread is marked ignored, KMail closed, new mail arrives in that thread, and then KMail is reopened, although all the old messages in the thread are still marked ignored, the new messages are not, and so show up as new.
See also #186853
Just seen it where I was viewing a folder with ignored threads, new mail arrived in those threads, and was not marked as ignored (instead it was appended as new mail to the thread). So you don't even have to close/wait/open Kontact to trigger this.
*** This bug has been marked as a duplicate of bug 186853 ***
Created attachment 42485 [details] Example failure