To be honest, I believe it was just Super Mario World. I didn't think to test another game since It didn't make sense to be a rom problem, but I definitely will in the morning and report back to the thread.
I checked the ribbon cable, and the solder joints of both ribbon cable connectors for continuity with ok results. I also gently ran a blade around a few of the joints/components to be safe. I also checked the vcc of the controller, it was normal at 4.96v. I saw some frequency going on with the data wires of the controller, but I wasn't sure what else I could do with those with a multimeter.
I would like to figure out the problem, but in the meantime since this is my only snes system, I ordered a replacement motherboard and controller ports to try to isolate the problem, and also give me a good working system when I feel like playing
.
Thanks for the replies.