With 3.4 kernel situation is same

uname -a
Linux ubu-test2 3.4.0-030400rc5-generic #201205011817 SMP Tue May 1 22:18:19 
UTC 2012 x86_64 x86_64 x86_64 GNU/Linux

lspci 
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)
00:08.0 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
01:00.0 VGA compatible controller: NVIDIA Corporation NV44 [GeForce 6200 
TurboCache(TM)] (rev a1)

I have same issue on other machines with other hardware configuration
including SuperMicro X9DRW-iF

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https://bugs.launchpad.net/bugs/991977

Title:
  Ubuntu 12.04 hangs on shutdown

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