Heya, Sentai... let me help you out with this new one.
The problem you're experiencing now... is one that we -all- are experiencing.
For some reason, there are these 'room' and 'portal' markers... which when placed, somehow manage to render anything within their boundaries invisible. Obsidian apparently used these quite a lot, as well, because there are numerous places in which it is nearly impossible to create a mod (for anyone like myself, anyhow, who lacks the skill to work around this problem) in that location.
I'm hoping that, at some point, they'll patch the GECK and fix this mess.
Hard to say for certain if that's ever going to happen though...
I wish I knew what those damn markers even -do-... >.<
The markers have a simple function: reduce loading.
Before I added the marker's, I would walk in to the cave and the game / my pc would uber lag because it was loading and rendering the ENTIRE MAP. With these specific markers, It only loads the "room" your in, the blue boxes indicating which room. The Portals are so that when you reach the end of that room, you can see in to the next one, if they aren't up, its just an empty space and it looks like you can walk through and keep falling, but it would actually just load the next "room". This way it cut's down on loading and you can still see so it doesn't look ugly / broken.