Hello, I need help....

About a month back, the System32 folder would automatically pop up once the computer was started up. On the window it would warn that the files were hidden because any changing of them could damage my computer.
After a couple of weeks of this happening, I did a system restore to the day before the System32 file popped up. The System32 did not appear, but every program that I had deleted "came back." I tried to delete them but a prompt told me that there was an error. SO I retracted my system restore back to its original "system32" pop-up state.
I figured it was a virus so I got kaspersky Anti-virus installed and deleted these Viruses:

backdoor.winet
download.trojan
W.32.aplore@mm
Trojan Horse

The Backdoor virus was in the System32 folder (and difficult for the virus scanner to delete automatically), so I followed the instructions from the kaspersky anti-virus site to completely remove it manually.
HOWEVER, the System32 folder still pops up and I am fresh out of ideas.

Please help!