I've discovered the cause of the issue. The system contains an i450NX
chipset which has peer PCI buses. To work around buggy BIOS situations
where these weren't discovered a fix-up was added that looks for and
scans them as secondaries of the first root bus.

This causes the later ACPI code to ignore them because they are already
in the pci_root_bus list.

I've developed a patch for testing which is attached to the bug at
kernel.org:

http://bugzilla.kernel.org/show_bug.cgi?id=10396#c18

The patch applies some DMI matching that looks for the Dell PowerEdge
6300 and if found, doesn't apply the i450NX fix-up. The system is now
undergoing testing to discover any side affects of preventing the buses
being discovered as secondaries.

$ uname -a
Linux PowerEdge6300 2.6.25-rc8-acpi-pci-bus #3 SMP Wed Apr 9 08:29:54 BST 2008 
i686 GNU/Linux

$ grep -i 'aac' /var/log/dmesg
[   76.282508] Adaptec aacraid driver 1.1-5[2455]-ms
[   76.282520] bus: 'pci': add driver aacraid
[   76.407282] bus: 'pci': driver_probe_device: matched device 0000:03:03.0 
with driver aacraid
[   76.407819] bus: 'pci': really_probe: probing driver aacraid with device 
0000:03:03.0
[   76.612034] AAC0: kernel 2.8-1[6099] 
[   76.613521] AAC0: monitor 2.8-1[6099]
[   76.617518] AAC0: bios 2.8-1[6099]
[   76.621520] AAC0: serial 8A0376
[   76.642288] driver: '0000:03:03.0': driver_bound: bound to device 'aacraid'
[   76.645545] bus: 'pci': really_probe: bound device 0000:03:03.0 to driver 
aacraid

-- 
-server kernel variant fails to boot on PowerEdge 2650 with AACRAID timeouts
https://bugs.launchpad.net/bugs/149071
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