Are the drives SATA or IDE? Also what version (including SP and edition ie. 32x or 64x) of windows are you running and what are your full system pecs?

Does the same thing happen if you boot with only your main HDD plugged in? Is the 2nd drive new or old? Did this only recently start happening when you started using this new drive (if it is new) or has the drive previously worked and only recently started having this issue?