I ran into a first yesterday. As seems to happen on a somewhat regular basis, a client had a virus infected computer. One of tools I normally rely on is TDSSKiller.exe from Kaspersky. It removes most rootkits that infect the boot sector of a hard drive. And is one of the few that checks the boot sector of non-boot drives. So, you can use it when a drive is externally attached.
In this case, TDSSKiller.exe identified Rootkit.boot.SST.b. When the software attempted to clean it, it didn't display an errors, but if you looked at the log it indicated that it couldn't be cleaned.
Some web sites suggested downloading Kaspersky Rescue Disk to remove it. This is a bootable linux CD/USB image. Basically, it accomplishes the same thing as placing the drive in an external case. It prevents any malware on the drive from loading in the boot process. This tool also found the rootkit, but couldn't remove it.
I also tried booting up in the XP recovery console and using FixMBR, which appeared to work, but the rootkit was still there.
The final fix was referenced by a few web sites. This rootkit created its own partition that it inserted into the boot process. None of the repair tools understood the boot process and therefore could not repair it.
On this computer, the OS partition was 40GB and a 100 MB parition was created after that. The 100MB partition was marked active and therefore was used to start the boot process. When viewed from within Disk Management, the partition type was unknown. The fix was to remove the extra 100 MB partition and then mark the OS partition as active. After this, the rootkit was gone.
Based on reading other web sites, the size of this partition may vary. I saw references to a small partition that is only a few MB. I'm guessing the virus authors changed it to be 100 MB to make it confusing with the 100 MB partition used by Windows Vista and Windows 7. Also, I can only assume that a larger partition provides more space to hide malware that is introduced during the boot process.
After removing the rootkit, there was still a bunch of other malware that I removed with MalwareBytes and SuperAntiSpyware. In the end the only thing lost was some Start Menu shortcuts.
Realistically, I should have just wiped it and rebuilt it, but after putting in an hour or so, it became competitive and I just wanted to win.