Mine was just an idea. If you're experiencing an extremely short burst that overloads the machine, it could be so short that it disappears when measuring average cpu load which is what most tools do, but it could affect a near realtime buffer write or read (from an audio or network card). If there is any way to plot very short high spikes it should become recognizable, especially if it obeys some regular pattern like a timed irq or the like.
In our old case, the hardware were Alpha workstations and Tru64 the OS, we nailed the problem to a driver because installing both Linux and *BSD on the same hardware the problem disappeared, so it can be a software issue.
