There is nothing in the game that can advance the PIDRNG over 1000 frames like that except rain, which isn't an issue inside a cave. Unless you turned on the C-gear and just stood there, the frame probably didn't actually advance 1110 frames. Are you sure you counted right? Got the right ID combo entered into reporter? Did the nature, gender, ability, and pokemon match up to any closer frames?
I am as thoroughly confused as you are. I've done numerous RNG's for nearly every stationary legendary in W2 so I know the ID/SID combo is correct, and even if it wasn't correct, that does not explain the random frame I keep getting. IIRC, Frame 112 is synch Quiet Ability 0 Male at encounter slot 0, while Frame 1222 is non-synch Bold Ability 0 Female at encounter slot 6, which is what I got. In fact, Frame 1222 is the ONLY non-synch Bold Female at encounter slot 6 within three thousand frames. That is why I am so sure it advanced 1110 frames as the alternatives are that it advanced by three THOUSAND frames or more.
As for the other things. Chargestone Cave, near Mistralton entrance (I don't think it is possible for the WNPS to affect me there), not raining, C-gear off. Heck, I even checked to see if it is a location based problem and I tried going to the basement of Chargestone Cave. No dice. I've tried a new seed and I'm still getting gigantic random frame advances. I'll record the data to see if it is a consistent 1110. At least then I can accomplish something.