I thing that the problem could be in Preloader and Device Tree Blob file (.dtb). The Preloader and ‘.dtb’ file predefined in image of SD card, which You use, probably does not include the rigth GPIO ports which You have specified in Your project.
So You need to generate Your own Preloader and ‘.dtb’ file according to Your unique system created in Qsys. Fortunatelly, it is quite simple procedure, You can find many guides on RocketBoards site, e.g. https://rocketboards.org/foswiki/Documentation/EmbeddedLinuxBeginnerSGuide.
I hope that this will be helpful.