Cefiro

What PID frame did you land on? You may have had NPCs advancing the PID frame.

Copy and paste your seed into the main window of RNG reporter, select Method 5 PIDRNG, and click "Generate", and finally right click, select "display characteristics", and enter the seeds IVs.

Look here

Essentially, you advance the PID to whatever frame that has the encounter slot pokemon you're looking for.

I read you needed help with encounter slots

Yep. That definitely explains why you were hitting different seconds. I fixed that problem from Pikatimer so I didn't know how you could hit differently. Is your avatar Ammy?