Dual Hard Drives will not boot

Hello,
I was using a 13GB old drive, when I decided I was going to put another drive in.
I made sure the 13gb was 'Master' and the new 40gb was 'Slave' but when I use both drives at once windows will not boot.
I removed the 13gb and installed windows on the 40gb and it works, but windows still will not boot when I have both in at once.
Please help?