Make sure that all drives are jumpered properly. Cable Select is the best choice. When using CS, the drive you want to be master MUST be on the end of the cable.
In BIOS Setup, be sure that you have the exact Windows drive set to boot. In the old days, you simply made the Windows drive the PRIMARY MASTER and chose SCSI if it was on a separate controller card. These days, you have to be specific about which drive boots.