Windows may see it as a drive partitioned with unrecognizable partitions and fail to show it in My Computer. But it may show the actual drive in the administrative tools (sorry, don't have Windows available to tell you what the actual tool is called).
I'm not sure what Windows seeing or not seeing the device has to do with anything. The BIOS does or you couldn't dual boot, unless you're dual-booting with a single drive. Maybe, if it's not a dual-boot from that second drive, the BIOS doesn't see it either. If the BIOS sees it, any linux installer, therefore, should see it.
Not sure what you're trying to accomplish. Maybe if you were a little clearer about what it is you need it would be easier to explain things or help.
Can a live CD see the drive? Does it show up in the BIOS? Are you sure of your connections?
Edited by stiltskin, 04 November 2011 - 10:07 PM.