Because of new encryption interfaces in kde, I am not sure if this still applies.
The fact that KMail blocks on any external action, be it pop3 transfers or external filter commands is a know issue. It is registered in kde bug tracking as bug #41514. http://bugs.kde.org/show_bug.cgi?id=41514 But I really think the changes in recent KDE versions should have leviated this issue. Kind Regards Anders E. Andersen