I would suggest putting the second hardrive as a SLAVE, not a master. Configuring it as a Master drive makes it the boot HD, but since you've got TWO, it would go haywire. Try making the second HD as a slave instead.
Note that I am assuming that you have Windows on Drive One as your main boot drive, and drive two as an auxiliary drive for general storage purposes. Please correct me if I am wrong. But if this is the case, try configuring the second one as a slave.
ComputerCop911
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