Code:
CPU0
0: 9390956 IO-APIC-edge timer
1: 4 IO-APIC-edge i8042
3: 11 IO-APIC-edge
4: 12 IO-APIC-edge
7: 0 IO-APIC-edge parport0
8: 1 IO-APIC-edge rtc0
9: 0 IO-APIC-fasteoi acpi
12: 1 IO-APIC-edge
14: 2689246 IO-APIC-edge ata_piix
15: 0 IO-APIC-edge ata_piix
16: 179014 IO-APIC-fasteoi uhci_hcd:usb5
18: 3897474 IO-APIC-fasteoi uhci_hcd:usb4
19: 890802 IO-APIC-fasteoi ata_piix, uhci_hcd:usb3
23: 1884482 IO-APIC-fasteoi ehci_hcd:usb1, uhci_hcd:usb2
26: 1180967 PCI-MSI-edge i915
27: 3942417 PCI-MSI-edge eth0
28: 13454 PCI-MSI-edge hda_intel
NMI: 0 Non-maskable interrupts
LOC: 38761815 Local timer interrupts
SPU: 0 Spurious interrupts
PMI: 0 Performance monitoring interrupts
PND: 0 Performance pending work
RES: 0 Rescheduling interrupts
CAL: 0 Function call interrupts
TLB: 0 TLB shootdowns
TRM: 0 Thermal event interrupts
THR: 0 Threshold APIC interrupts
MCE: 0 Machine check exceptions
MCP: 909 Machine check polls
ERR: 0
MIS: 0
I've been tracking it by a canary (which seems to be a symptom):
Sep 17 06:11:08 silver-dragon rtkit-daemon[23904]: The canary thread is apparently starving. Taking action.
Sep 17 06:17:14 silver-dragon rtkit-daemon[23904]: The canary thread is apparently starving. Taking action.
Sep 17 06:21:48 silver-dragon rtkit-daemon[23904]: The canary thread is apparently starving. Taking action.
Sep 17 06:32:43 silver-dragon rtkit-daemon[23904]: The canary thread is apparently starving. Taking action.
Sep 17 06:34:42 silver-dragon rtkit-daemon[23904]: The canary thread is apparently starving. Taking action.
Sep 17 06:38:42 silver-dragon rtkit-daemon[23904]: The canary thread is apparently starving. Taking action.
Sep 17 06:39:28 silver-dragon rtkit-daemon[23904]: The canary thread is apparently starving. Taking action.
Sep 17 06:43:08 silver-dragon rtkit-daemon[23904]: The canary thread is apparently starving. Taking action.
Sep 17 06:46:32 silver-dragon rtkit-daemon[23904]: The canary thread is apparently starving. Taking action.
Sep 17 07:01:22 silver-dragon rtkit-daemon[23904]: The canary thread is apparently starving. Taking action.
Sep 17 07:08:34 silver-dragon rtkit-daemon[23904]: The canary thread is apparently starving. Taking action.
Sep 17 07:34:20 silver-dragon rtkit-daemon[23904]: The canary thread is apparently starving. Taking action.
Sep 17 07:47:23 silver-dragon rtkit-daemon[23904]: The canary thread is apparently starving. Taking action.
Sep 17 07:48:35 silver-dragon rtkit-daemon[23904]: The canary thread is apparently starving. Taking action.
Sep 17 08:35:12 silver-dragon rtkit-daemon[23904]: The canary thread is apparently starving. Taking action.
Sep 17 09:29:11 silver-dragon rtkit-daemon[23904]: The canary thread is apparently starving. Taking action.
Sep 17 10:38:09 silver-dragon rtkit-daemon[23904]: The canary thread is apparently starving. Taking action.
Sep 17 10:45:56 silver-dragon rtkit-daemon[23904]: The canary thread is apparently starving. Taking action.
Sep 17 10:47:15 silver-dragon rtkit-daemon[23904]: The canary thread is apparently starving. Taking action.
Sep 17 10:57:34 silver-dragon rtkit-daemon[23904]: The canary thread is apparently starving. Taking action.
Sep 17 11:21:05 silver-dragon rtkit-daemon[23904]: The canary thread is apparently starving. Taking action.
Sep 17 13:52:37 silver-dragon rtkit-daemon[23904]: The canary thread is apparently starving. Taking action.
Sep 17 13:53:35 silver-dragon rtkit-daemon[23904]: The canary thread is apparently starving. Taking action.
Sep 17 15:18:42 silver-dragon rtkit-daemon[23904]: The canary thread is apparently starving. Taking action.
I've had my dad unplug most of his USB devices to see if it was one of them. (as he has hubs, upon hubs plugged into each other)