@Darkrai's nightmare: Just to add real quick on what hipoke said before you go back to the drawing board, but one small yet important measure you should consider is that you're doing hard resets for your parameter searches. There's a fourth parameter (GxStat) that the game keeps at a value of 6 for "regular" startups, and because it fluctuates during soft resets (I don't know how erratic it is or if you can calibrate for it), PPRNG doesn't bother with it and assumes the user is doing hard resets for multiple trials with parameters or Pokémon. It's kind of a trivial thing, but I know a fair few people who have been screwing up for a while because they've carried their 4th Gen RNG and general convenience habits over to 5th Gen RNGing without a second thought, soft resetting being probably the biggest one. Other than that, just changing your date/time and in-game capture environments is recommended anyway for parameter calibration, so if you messed up a particular time without noticing or anything else bizarre comes up, you could just consider it an accidental blip in the system (some things just aren't researched enough yet
…).