No, I don't really know, but it sounds like it might have had something to do with the Microsoft Fix IT we ran, and a reboot was required to finish the fix.
No, I'd leave it disabled, you'll keep your computer more secure by doing this.
3. What's next? I guess I turn Auto Play back on?
You can take a look at this thread to see what G2G recommends.
BTW, the latest Consumer Reports rates Avira as the best free anti-malware program. I've been using Microsoft Security Essentials. What does geeks to go recommend?