revisting this problem:

In my dmesg on 2.6.31:
[    0.149369] pci 0000:08:00.0: reg 10 32bit mmio: [0xe8000000-0xefffffff]
[    0.149459] pci 0000:08:03.1: reg 10 64bit mmio: [0xe0500000-0xe0500fff]
[    0.149528] pci 0000:08:04.1: reg 10 64bit mmio: [0xe0501000-0xe0501fff]
[    0.149569] PCI: peer root bus 08 res updated from pci conf
[    0.149590] pci 0000:09:00.0: reg 10 32bit mmio: [0xe1000000-0xe1ffffff]
[    0.149595] pci 0000:09:00.0: reg 14 32bit mmio: [0xf0000000-0xf7ffffff]
[    0.149607] pci 0000:09:00.0: reg 30 32bit mmio: [0x000000-0x01ffff]
[    0.149646] pci 0000:08:01.0: bridge 32bit mmio: [0xe1000000-0xe1ffffff]

whereas on 2.6.28 the line "PCI: peer root bus" is no there, instead
this is where my USB hubs are detected.

-> This PCI: peer root bus updating fails on my machine and lets some
PCI devices (in this case my USB) disappear.

adding pci=noacpi solved the problem for me, however this seems to be a
hack rather than a fix.

-- 
USB disappears after upgrade to 2.6.31 kernel
https://bugs.launchpad.net/bugs/464452
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