Welcome to INTEL forum. Could you help verify the Switch and Jumper Settings are in default factory switch settings for the Intel Arria V GX FPGA Development Kit and try the BTS test again.
No, they do not match the settings in that ug_... since it is not the board that I have. But they *do* match the ug for my board, shown in the image above as P/N 6XX-44099R, and on the box as DIK-START-5AGXB3N-0S. The ug I used is "Arria V GX Starter Kit", UG-01117-1.2, Feb 2013, page 18, Figure 4-1. But that is only a secondary point. My board does not *have* a 5AGGXFB3, and I can not find that part # anywhere on the internet. If it is actually looking for that ID it will have to keep looking for a long time. There may also be other problems, but this should probably be cleared up first.
I also had to install Quartus V15.0 so I could get some work done, since the link for V12.1sp1 was defunct for so long. I have renamed that directory so that it can no longer be found and changed the Environment Variable to point back to V12.1sp1. (although I can't imagine why a pre-compiled program would need a particular version of the development software to work). Still doesn't work. Possibly because it doesn't change a 5AGX into a 5AGGX. Anybody who *has* gotten this to work must have that elusive 5AGGX. Where can I get one?