Sometimes reboots can happen because of heat build up and sometimes because of malware. Did this problem occur prior to the rootkit infection? Are there any other signs if infection?
Try scanning with the free version of AVG Antispyware
http://free.grisoft.com/doc/20/lng/us/tpl/v5To boot into safe mode, see if this works
> Click Start, Run, then type MSCONFIG in the box and click OK
> The System Configuration Utility appears, On the BOOT.INI tab, Check the "/SAFEBOOT" option, and then click OK and Restart your computer when prompted.
> When you're finished open MSCONFIG again, on the BOOT.INI tab, uncheck "/SAFEBOOT" and click OK to restart your computer