I actually had issues trying to print the inlays for some N64 covers as well. My printer just didn't like the settings being tampered with. I eventually ended up just printing the inlays on a separate sheet, cutting them and then placing it on the inside of the case and it ended up looking pretty nice. Even opening and closing it multiple times you can't really tell it's a separate piece. The additional weight also makes the case just feel a bit better in my opinion.
I'm using Red River Matte photo paper (1514) incase that helps.