2013 Scion FR-S Automatic Shifter Problem
 

I know. An automatic FR-S is a cardinal sin. I repent in sackloth and ashes.

The problem I'm having is that the knob won't shift up or down in manual mode, while the paddles shift just fine. I've been looking around online but haven't seen a solution and figured I'd ask here.

Has anyone had/heard of issues with this?

I haven't heard of or had that particular problem, but then I think I've used the knob for manual mode maybe once. I usually use the shifters.

So clearly you can narrow it down to that shift cluster, so it's either partial software issue or hardware issue in that shifter. I'm not sure what the part number is for that but it could be tester by removing and plugging in a shifter from a junkyard 14,15,16 or using the OEM techstream guide to troubleshoot it.

frs shifter problem
 

I found the problem with your shifter
https://www.youtube.com/watch?v=cQbXFzstPjQ