no, the placement dosent matter. As long as it is either completely vertical or completely horizontal, and fastened securley. Is it the same sound that comes out of other computer?
What kind of HDD is it? Western Digital? I had a problem with a WD drive that it made a loud clunking noise, at a steady interval. i wasnt sure what it was, but whatever it was, I hated it. It sounded really bad, like things were breaking. I FREAKED the first time I heard it. So i sent it back and had it refurbished. Know what? Same sound when I got it back. I didnt know what to make of it. But, akin to the idea of ignorance is bliss, I ignored it and it went aweay. My dad is currently using that hdd, and it has been almost three years since the 'incident'. Drive working fine, I dont think it has ever crashed either. Come to think of it, about a month ago I installed XP (from 2000). Clean install, no problems.
It may not be bad, just an annoyance that sounds really bad. Like was said earlier, see if you can record it and post it. If you do that though, dont use a crappy microphone. Use something good.