Aaahhh right. I might know what's the problem. Did you use the book 'Passages of Ma' habre' during this playthrough? I was pretty sure that it caused the bug. Upon the Ma'habre timer running out, the screen goes black and you return to normal world. The trigger that makes the screen go black is still left there if you load the same save, but starting a new game should fix it.
If you don't want to go through the entire game again, apparently you can make things visible again by finding the beacon of the depths and using it.
Sorry for the trouble D: