have you tried going into bios and setting the boot priority? setting primary hard disc as first device?
have you tried unplugging your "slave" secondary drive and booting without it?
have you tried unplugging everything such as external drives , key board , mouse etc then seeing if it will boot ok?
are they sata drives? (serial ata) (they have no master and slave)
If we can get to the bottom of the boot issue first we can resolve the drive not showing issue next