It's probably your Timer0. What spread are you using, along with the keypresses?
I'd recommend doing two calibrations for parameters, one for no keypresses, and one for three keypresses.
Does the program still warn you if you'll get thousands of results?
Reason being, I accidentally hit 'Search' before I filled in my desired IVs for 'Egg Seed Searcher', and obviously thousands of results starting popping up. Couldn't hit Stop because the program stopped responding, and the comp started lagging incredibly. After a couple minutes of the whole computer being frozen I managed to bring up the Force Quit and kill it. Lost some results I had yet to save, too. Joy.
A nasty mistake on my part, but yeah, is that feature still in the program?