couple of things you could try.
First of all, it sounds like you may have the FakeAlert malware. I've seen that some stuff up bad.
If possible, boot into safemode with networking and go download Malwarebytes. (just do a google search for it). I'd recommend superantispyware but it wont install in safemode.
If that doesnt work, boot off of your Windows install disk. It will ask if you want to repair or continue installing windows, dont hit "R" at that point.... Keep acting like your going to install windows as a fresh install and at some point its going to search for a current windows installation..... when it finds it, it will give you another option to repair by hitting "R".... do that..
again, if you hit "R" from the get-go it will take you to a command console, you could try doing chkdsk /r from that but it probably wont help. If you get to that command console, you didnt go far enough into the install. You want to get to the point where it scans for current windows installs, then hit R when it finds your OS on the drive, just before you do a fresh install.
It will look like its formating the drive and reinstall windows but it wont (if you do it right), its just deleting the windows files and replacing them.... Your profile and programs will all stay intact. Again, its just restoring all off the windows core files.
After that repair is done, go download superantispyware. just do a google search for it. its free. let it do a a complete scan.
If after all that you still have problems, let me know via PM.... Seriously, I do this for a living and am not some freelance worker who will tell you that you need to format the drive. Dont take it to some place like Best Buy's geek squad... I run circles around them by myself. I deal with this on a daily basis at a government ins ute and have only had 1 time where a reload was necessary.