New error when programming device: "Unable to scan device chain. On-board programming hardware is disabled."

FYI: I used Quartus 14.0 to compile the Avalon design, and the 2nd FPGA I have been using would program even though when I turn it on it doesn't load the factory default settings like trying to connect to the BUP, but was always still able to program the board with Quartus up until now, recently I had been inserting the FPGA into a PCIe slot on a Linux CPU host but since the Hard IP isn't configured, no communications have been made to the board that way so I don't believe that is the issue.