I assume you have a MXI link (MXI-3 or MXI-4) connecting your PC to a PXI chassis. In this case, the only supported way of power-cycling the PXI chassis is to power down the host computer, cycle power on the PXI chassis, and then power up the host CPU again.
Power cycling the PXI chassis with a live host severs the PCI bridge connection to the PXI chassis. Most computers, and OSes, won't expect this to happen since all devices on that PCI bus are usually restricted to the same chassis (powering down and up at the same time). Think of it as removing a limb while you're still awake. Rebooting the PXI chassis with the host computer still active will often result in a hang though the behavior would be system specific.
