Background info: I use the mod "Colorful lights no shadows" to lessen the load on my CPU. It changes all of the shadow lights (Shadow_Spotlight, Shadow_Omnidirectional, etc.) to "Omnidirectional". This replaces the dynamic shadow-casting lights with static-shadow lights. This also removes that ugly blockiness.
Reverting the lights to shadow casting lights remedies the issue.
The issue is that the textures of particular surfaces are made pure black, with only the normal maps being used. If lights are used (a torch, the spell candlelight), their colour can be somewhat reflected.


It's not light specific. It pertains to certain cells only. Hjerm (before Blood On The Ice quest is done. Haven't tested after it is done) and Bleak Falls Barrow (the altar between Arvel The Thief and the draugr) are two that I've found so far.
On a side note, the toony effect is awesome. If only it were possible to render the textures as well...
Edit: Forgot to upload the mod. Here it is.