I don't see any make, model but if it's a desktop I power down and unplug the mouse and keyboard (on a laptop it's mildly harder to do this) and try again. I've lost track of stuck keys.
http://answers.microsoft.com/en-us/windows/forum/windows_vista-system/computer-shuts-down-slowly-and-boots-to-advanced/0ad7b51e-e1ae-46ba-880a-0d6d7b540fe2 repeats the SFC but with a twist about RUN AS ADMIN.
An infected boot area could do this but before we try to repair that I have to write to be sure your backups (plural!) are current. Then go get EASYBCD and repair the boot areas.
When I turn on my computer, It ALWAYS boots up to the "advanced boot options" screen first. No buttons are pressed. Is there a command line somewhere I can change.
I ran chkdsk, no problems, and the sf /scannow command, and both said all was good.