I have my junk settings in both Account Settings and Security Options set to have junk email sent to the "Junk" folder. Incoming emails will automatically (and accurately) be marked as "junk", but remain in my inbox. Emails that I manually mark as "junk" also remain in my inbox. I turned off all junk settings and then turned them back on, restarting my computer each time changes were made, but the problem persists. The settings had worked fine for several years, but a couple weeks ago the problem popped up and nothing has automatically gone to "junk" since.