Your PID (shiny) Frame will be somewhere between 38 and 60. If there are wandering trainers on the route, even if off screen, the PID will advance randomly.
You need to first use the program's Calculate Initial PID button to get this 38-60 number. In one example, my starting frame was given as 43.
Then, you need to figure out the shifted frame (this pid frame may have been shifted because of wandering trainers). Just do some test runs (ie don't do hundreds of chatters each time). Just do a run where you do 0 chatters immediately, and on the next run do 1 chatter, maybe a 2 chatter run, etc, and find the pattern of natures on the generated table. Assuming you hit your seed, you'll find the pattern and determine the shifted starting frame.
What Pokemon are you abusing? Gifts still? I'm rusty, but I hope this helps.