Setting up PCIe Connection Cyclone V

Hello, I have tried lowering the TCK frequency to 16MHz.

As of right now, I have tried programming the .sof directly and Quartus reports the programming was successful. However, the board is still not detected by the Linux machine (tried with no reboot, soft reboot, hard reboot).

I have also successfully uploaded the flash file now (both through the Nios II EDS terminal and through the Board Update Portal). But on power-up there is no change in what lspci reports.

I believe the .sof file and the flash file upload & programming cause the board to have the same behavior because there are 8 LEDs that are lit upon factory reset. However, when I write to the board in any of the above ways, exactly 3 of these LEDs remain lit. The board update portal also no longer comes online unless I flip the FACT switch and have the board powered up such that it has factory default settings.

I am not sure where to look for any mistake. Is there a different example I could try to use for the PCIe interface? I was able to program a different example I made that just connected some of the LEDs to buttons on the board. I confirmed its success when the buttons still effected the LEDs after a reboot.

Thanks for any assistance you can provide,

Best regards, Alex