Hi, thanks for the feedback. That should be the correct timing most of the time. The only exception is on Synth Wizard, where it's two beats (the rock appears -- next beat it starts blinking, next beat player jumps), sorry if that's not clear.
Also, if it's not working that way for you, and you're playing on an emulator, try calibrating again.
The keyboard warning is there because the game plays better on a real GBA, a handheld device, or a gamepad. Most of the time you need to lock your aim, point and shoot, and due to N-key rollover issues it might not work depending on how you set up keys.