Are there any unusual or experimental device drivers running on your system? Kernel mode device drivers operate in the context of other processes, and normally don't have processes of their own. A poorly-written kernel mode device driver can eat up CPU time in an interrupt handler, for example, and this wouldn't show up on task manager if the interrupts were happening while the system idle process was running.
Something else to check -- could it be your hard drive? I once had a system with a faulty hard drive controller, that would fail some commands after a lengthy timeout. Since Windows accesses the hard drive all the time, even when the system is mostly idle, sometimes an access during idle would block the hard drive and the system would become extremely unresponsive.
