But at last, after over 300 hours of gameplay and about 5 different characters, I have discovered the source of the noise: NIRNROOT!
Seriously. I have been confounded by this mysterious noise for months, and after slaying the cave troll before the road to Ivarstead, I found a glowing Nirnroot creating the chime noise. Wouldn't have guessed a plant was making the noise. But that's all for now, just thought that perhaps some people hadn't discovered this and were as confused as I.

If it's something else maybe someone else will tell us. 

Knew it was nirnroot since oblivion, also playing with headphones helped. But seriously didn't you see the white glow when that sound was heard?