sky2: fix PM related regressions

Fix the problems reported for 2.6.27-rc1 caused by over aggressive
power management. Turning clock off on PCI Express is problematic for WOL,
and when doing multi-booting.

Signed-off-by: Stephen Hemminger <shemminger@vyatta.com>
Signed-off-by: Jeff Garzik <jgarzik@redhat.com>