Had this happen to me last night. I thought something was just sitting on W (because I was moving my laptop, with mouse/headset/phone/ipod sitting on the keyboard) but after moving my stuff and pushing buttons and my character kept running. Figured she was training for the Cyrodiil 5k.

This has ALWAYS been the case for me. It makes me sad.

I can think of a few reasons:
Something on the key. Don't laugh, happens more then you think.
The keyboards sensors are not properly working and still registering the key as "down" even though it is up. Generally it is the releasing of keys that fires the action.
Key Ghosting and Jamming
You have a wireles keyboard and some interference in the Radio ways (this has been reported with other Keyboard and mouse related bugs). Also check the batteries (of course).
Misscomunication between client and server. Basically you client registered stop of autorun, but somehow the server did not get it. And server overrules client in such maters. This should only happen if you already experience lag overall.

I get this every now and then. I thought it was my keyboard at first, but it doesn't happen in other games, typing, etc. I don't have auto run bound to anything, nor do I use a wireless keyboard.

I dunno why this would be, but I've had this issue in multiple MMOs, not just this one. Tapping the direction that you're moving in usually fixes it.