Re: How to find if BIOS has already enabled the device

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The offending code is in hcd-pci.c - which seems to be executed unconditionally. usb_hcd_pci_probe() calls pci_enable_device() which hangs if there was already a device present, attached to the controller.
Have you attempted more generic fix-hardware-hang solutions? I've known more than a few times where a good old "noapic nolapic" snapped a box out of some strange and seemingly unrelated problems...

Also, is your BIOS fully up to date/modern? A quick Google search found a few things like this:
http://www.techspot.com/vb/all/windows/t-18940-USB-Hub-And-Boot-Problems.html
The problem might be more generic than a bad interaction between drive and kernel.

~John Livingston
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