I was under the impression that since I just searched for the IVs under those encounter slots it would be PIDRNG frame 1, I'm begging to realize that may be completely wrong.
You have overlooked the fact that the starting PID frame is somewhere around the 40-60 range, not 1. There's a button right on the main RNG Reporter window that will tell you the starting frame for the particular seed that you're using. That is the first frame that it's on when you turn the game on, and it increases from there. So yes, you were likely on frame 55.This means I very likely was on PIDRNG frame 12 unless it's somehow possible to have gotten to 55.
Also, for your own convenience, search for seeds on IV frame 1. Doing advancements to increase the IV frame only complicates every other step of the process. IV frame advancement is (IMO) sort of an antiquated process that people did before we had as much control over the PID (before Chatot cries were discovered). Now if you ever have trouble finding a seed, you can just search for a higher PID frame.