-d 0 -f book.dat -t _3600 threads=4,pondering,maximize_score

This is the only pachi.exe that exists for Windows, on a 4-core CPU, Win7, Drago 4.21

When I click to make my move, the board is very slow to show my stone. It also seems like it takes some time after pachi makes the move until the stone actually shows on the table.

The pachi settings are designed to maximize CPU usage: use all cores, think while the opponent is thinking. The CPU is at 100% all the time.