Combofix is excellent in removing rootkits. I used it a couple of times years ago and it worked like a charm! I guess there is more than one type of exploit that targets the explorer.exe process. I had this problem earlier this month. In my case the pc I was trying to fix was creating at least one more explorer.exe which ate up all available memory pretty quickly and started displaying large ads covering the desktop. (It would create even more explorer.exe sometimes) It basically made the whole desktop background a giant ad display, like webpages with a bunch of "useful" links and banner ads changing every few seconds. Sometimes the background would turn just white for a while before the ads showed up. The computer became very slow and unusable. It was possible to close the explorer.exe with task manager but it kept returning within seconds if I didn't end the legitimate explorer.exe as well, which makes it hard to download software to fix the problem, but it's possible to restart "explorer.exe" from the task manager file, new task run menu. It was a pain though. I was fixing it remotely which made it more annoying too.
I was sure it must be a rootkit since system restore didn't solve the problem. Malwarebytes, the gold standard in malware removal came up with nothing. I think this rootkit can hide for a while before it starts going crazy with the ad displays. The computer was infected a month earlier and I thought I had cleaned it using system restore and Malwarebytes.
So after reading the above posts I decided to try Kaspersky TDSSKiller.exe Rootkit remover. I managed to run it and was delighted when it found a BOOT SECTOR virus "Rootkit.Boot.Cidox.b"! It removed it with no problem, and the problem was solved. No wonder no standard tools find anything, since this type of exploit writes itself onto the HD's boot sector, and that's not a file that can be scanned. In fact, I think that even re-installing windows without rewriting the boot sector, would leave this exploit intact.