i have a similar problem. Sometimes the USB ports stop working after a while.
 i use 2.6.32-33-generic kernel and prosessor is AMD athlon xp 1800+ is 

kernel.log say
 [    2.723602] usbcore: registered new interface driver hiddev
 [    2.740064] input: Compaq Compaq Internet Keyboard as 
/devices/pci0000:00/0000:00:11.2/usb7/7-1/7-1:1.0/input/input4
 [    2.740548] generic-usb 0003:049F:000E.0001: input,hidraw0: USB HID v1.00 
Keyboard [Compaq Compaq Internet Keyboard] on usb-0000:00:11.2-1/input0
 [    2.740808] irq 17: nobody cared (try booting with the "irqpoll" option)
 [    2.740816] Pid: 61, comm: udevd Not tainted 2.6.32-33-generic #72-Ubuntu
 [    2.740820] Call Trace:
 [    2.740839]  [<c058960e>] ? printk+0x1d/0x1f
 [    2.740851]  [<c01a246c>] __report_bad_irq+0x2c/0x90
 [    2.740856]  [<c01a0b84>] ? handle_IRQ_event+0x54/0x150
 [    2.740861]  [<c01a2620>] note_interrupt+0x150/0x190
 [    2.740867]  [<c01a2c2c>] handle_fasteoi_irq+0xac/0xd0
 [    2.740877]  [<c01059ed>] handle_irq+0x1d/0x30
 [    2.740887]  [<c05901dc>] do_IRQ+0x4c/0xc0
 [    2.740896]  [<c021a389>] ? sys_poll+0x59/0xc0
 [    2.740901]  [<c0103a30>] common_interrupt+0x30/0x40
 [    2.740904] handlers:
 [    2.740907] [<c0447db0>] (usb_hcd_irq+0x0/0x80)
 [    2.740922] [<c0447db0>] (usb_hcd_irq+0x0/0x80)
 [    2.740928] Disabling IRQ #17
 [    2.801023] usb 7-2: configuration #1 chosen from 1 choice
 [    2.849279] input: Compaq Compaq Internet Keyboard as 
/devices/pci0000:00/0000:00:11.2/usb7/7-1/7-1:1.1/input/input5
 [    2.850037] generic-usb 0003:049F:000E.0002: input,hiddev96,hidraw1: USB 
HID v1.00 Device [Compaq Compaq Internet Keyboard] on usb-0000:00:11.2-1/input1
 [    2.863643] input: B16_b_02 USB-PS/2 Optical Mouse as 
/devices/pci0000:00/0000:00:11.2/usb7/7-2/7-2:1.0/input/input6
 [    2.864104] generic-usb 0003:046D:C024.0003: input,hidraw2: USB HID v1.10 
Mouse [B16_b_02 USB-PS/2 Optical Mouse] on usb-0000:00:11.2-2/input0
 [    2.864182] usbcore: registered new interface driver usbhid
 [    2.864433] usbhid: v2.6:USB HID core driver

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Title:
  USB stops working after a while

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