Wahhey, problem on the thinkpads solved. Turns out to be a bios setting that must be turned off. Its the PCI Power Management that is causing the problem. Personally I think the kernel should be able to handle this properly, i.e. power back up the pci subsystem to enable access to the adapters.
This may take some hacking around to achieve, so for the moment if you're having this problem, simply turn off the setting in the bios.