I just heard back from Spiderco. The good news is that they're going to evaluate it and replace it if there is a problem. There really wasn't any fuss or pushback either...they were very happy to help and made mention that the rods are sometimes warped from new (an issue I'd heard of but I don't think this is my problem)

The bad news is that I'm going to have to ship it to them in Colorado out of my own pocket : (

That's warranty I guess.

I'm going to use the down time to try and source the diamond rods. If it's determined that the angles are out, I don't want to spend a crazy amount of time re-profiling all my knives again.