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Please Help ASAP, Urgent, Messed up computer

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Hi, I was helping my girlfriend get rid of her rootkit virus tonight.
I followed this guide http://www.geekstogo...40#entry1567240
After Running ComboFix windows booted up and every program she tried to run came up with error saying:
"illegal operation attempted on a registry key that has been marked for deletion"

She then proceeded to reboot her computer and it started a disk check and began going through many files...She said it would not allow her to cancel this.
I am out of state trying to help her, so am not sure exactly all the details...
She went ahead and went to bed and I told her to call me in the morning before she touched her computer...

Have I seriously messed something up here or did this computer just need a restart after running ComboFix?

Please Help :)
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