Arria GX + PCI express IP card powers down the PC, instead of just restarting.

Check that the PCIe reset pin is defined and used, rather that not defined and defaulted to output driving low. I have also seen the power-cycling thing happen when i have a card plugged into certain spots but not programmed. My best guess is an impedance matching issue of the card in config mode and the pcie trying to detect receivers, but it only happens sometimes in certain slots and then only sometimes. Also make sure you don't have a bootloader that is reloading images when you try and use the jtag. Let us know what you come up with.

Also you can go back to a version that worked and work your way up with the changes and see if any break it, although it seems to be a more root level problem rather than a higher level core functional change.

kevin