Version: 1.9.1 (using KDE KDE 3.5.1) Installed from: Fedora RPMs Compiler: gcc (GCC) 4.0.2 20051125 (Red Hat 4.0.2-8) OS: Linux Like bug # 99861, new messages from an online IMPAP acccount are marked read after piping them through e.g. spamassassin. When you look closely at the status bar, you see that the mail is downloaded from the Inbox, and uploaded again after spamassassin has done its job. After the upload the whole account is checked/synced and then the message is shown as "read". This way it is easy to miss replies to older mails when "Thread messages" is turned on.
This happens to me for any filter applied to new mail, not just those with a "Pipe through" action.
In the current version I don't have this behaviour any more.