When it's finished, it will boot to your normal startup/lock screen and you can login normally and then see if things are working correctly again.
Second, if you want to run a good scan for malware, click on the link below and follow all the steps to the letter, in the order they're given:
“Expand” the post titled: "Please try this" at the link below:
http://www.cnet.com/forums/post/f742c795-5881-433b-a29b-6d758efe5cd3/
Hope this helps.
Grif

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