I am having this issue with a fresh install of Ubuntu 9.04 AMD 64

lspci reports:
00:00.0 Memory controller: nVidia Corporation CK804 Memory Controller (rev a3)
00:01.0 ISA bridge: nVidia Corporation CK804 ISA Bridge (rev a3)
00:01.1 SMBus: nVidia Corporation CK804 SMBus (rev a2)
00:02.0 USB Controller: nVidia Corporation CK804 USB Controller (rev a2)
00:02.1 USB Controller: nVidia Corporation CK804 USB Controller (rev a3)
00:06.0 IDE interface: nVidia Corporation CK804 IDE (rev f2)
00:07.0 IDE interface: nVidia Corporation CK804 Serial ATA Controller (rev f3)
00:09.0 PCI bridge: nVidia Corporation CK804 PCI Bridge (rev a2)
00:0a.0 Bridge: nVidia Corporation CK804 Ethernet Controller (rev a3)
00:0b.0 PCI bridge: nVidia Corporation CK804 PCIE Bridge (rev a3)
00:0c.0 PCI bridge: nVidia Corporation CK804 PCIE Bridge (rev a3)
00:0d.0 PCI bridge: nVidia Corporation CK804 PCIE Bridge (rev a3)
00:0e.0 PCI bridge: nVidia Corporation CK804 PCIE Bridge (rev a3)
00:18.0 Host bridge: Advanced Micro Devices [AMD] K8 [Athlon64/Opteron] 
HyperTransport Technology Configuration
00:18.1 Host bridge: Advanced Micro Devices [AMD] K8 [Athlon64/Opteron] Address 
Map
00:18.2 Host bridge: Advanced Micro Devices [AMD] K8 [Athlon64/Opteron] DRAM 
Controller
00:18.3 Host bridge: Advanced Micro Devices [AMD] K8 [Athlon64/Opteron] 
Miscellaneous Control
01:02.0 Multimedia audio controller: Creative Labs SB X-Fi
05:00.0 VGA compatible controller: nVidia Corporation GeForce 8600 GT (rev a1)

and lsusb reports:
Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
Bus 002 Device 003: ID 046d:c041 Logitech, Inc. 
Bus 002 Device 002: ID 045e:00db Microsoft Corp. Natural Ergonomic Keyboard 
4000 V1.0
Bus 002 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub

-- 
USB devices are not powered off at shutdown (Dapper, 2.6.15)
https://bugs.launchpad.net/bugs/42149
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