Usually if bios can detect, linux can see the harddisk. Booting with knoppix, you will see all listed partition on desktop. If your hd is okay, the partition will show up.

Anyway you could try run this utility which comes with knoppix:
tesdisk
see if it can detect your 2nd hd.

You could try switch ide slot of your 2nd hd with 1st hd, try autodetect... just to check your ide port is okay.