Just what Herb said.
When you set the camera to fill flash ( IN + ), what you are telling the digicam is that you want it to fire it's own, on board strobe, every time it captures an image.
When you set the strobe to to PRE, you are warning the YS 90 DX that the Oly c4040 sends out a preflash to help determine the proper exposure (this preflash is needless in your case because of your manual strobe). Since you have a manual strobe, the YS 90 DX, when set to PRE, will be instructed ignore this preliminary burst of light and to coordinate, or sync, to the next, or main flash. The main flash fires in unison with the shutter and the YS 90 will pick up on this signal and fire as a slave , simultaneously.
hth,
bob