I had this problem aswell, but I had a 20GB hd as bootable with OS3.9 and the 2nd one was only 2.4GB used for backups.
No matter what I did I couldn't get the 2nd hd (on the same chain as the other hd) to auto mount. It didn't bother me that much because it was a back up, but I know it must be annoying you.
Re-installing and formatting won't make a difference. I do vaguely remember a "mount on boot" option somewhere but I couldn't honestly sya where it was, or even if it was for an hd.
Leave the hd as it is, I'm almost positive you won't need to reinstall/format it.