Cache, cookies and history are not clearing when I close Firefox even though they are set to do so and have been for ages

I recently had an update (or upgrade?) for FF 16. Today (and I believe the update was done a day or two ago?) my cache, cookies and history are not clearing when I close FF. Also, certain links are not working. Not links for full web pages but for site pop-ups (like the smilie window on a message board). They worked a few days but are not working today. I click the link and nothing happens. I noticed the problem with the cookies not clearing for a few weeks ago but it was only on one site not all sites which is what's happening now.
My apologies if that's a little confusing. Thanks!

At any rate, have you tried running Firefox in Private Browsing mode? This will ensure that no infromation from your session is saved once you exit Private Browsing mode and/or exit Firefox.
You can set Firefox to always start in Private Browsing mode: https://support.mozilla.org/en-US/kb/private-browsing-browse-web-without-saving-info#w_how-do-i-always-start-firefox-in-private-browsing

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