As a result of the high clock rates used, PCI-Express devices can take a lot of power even when they are idle. “Active state power management” (ASPM) was developed as a means for putting those peripherals into a lower power state when it seems that there may be little need for them. ASPM can save power, but the usual tradeoff applies: a device which is in a reduced power state will not be immediately available for use. So, on systems where ASPM is in use, access to devices can sometimes take noticeably longer if those devices have been powered down. In some situations (usually those involving batteries) this tradeoff may be acceptable; in others it is not. So, like most power management mechanisms, ASPM can be turned on or off.
via PCIe, power management, and problematic BIOSes [LWN.net].
This might have something to do with the PCI ethernet card being shutdown on medusa — a problem which has only been resolved by not using the PCI eth slot on medusa’s motherboard.