HD space, documents and programs disappearing rapidly.

About 3 months ago i noticed files on my harddrive that were not familiar to me. Mostly recycle bin's with an ? at the beginning and end of them. Then i noticed as i would shut down the computer, it would be downloading and installing updates i was unaware of. I checked my settings and auto install was not selected. i did a system restore and found files missing i didn't even know were gone. So i took it a step further and ran a program for lost or deleted files and was blown away to find about 40 gigs worth of stuff i didn't realize was missing because my hard drive space hadn't changed. Well somewhere along the way i triggered whatever was in my computer and it woke up fighting mad. I was locked out of files and directories. I no longer had an administrator account, but rather had administrator privileges still. Insteads of three profiles i now had one. I have been fighting this for so long and have used so many different programs to find, fix, fight this its rediculous.
I finally started to use reformatting as my weapon of choice to just start fresh. Well that got old after the tenth time. Long story longer...i don't know what it is. I found traces of remote access to and from my computer. i've found traces of commands to delete my files and replace with other stuff. I don't know what else to do, so i'm here asking for help.

 

Does anyone have any ideas about what this might be? I would really appreciate the help. Thanks in advance.