TRaK, I just realized something! I didn't notice this in-game when you were showing me, but the lights on the ceiling disappear too. I was also noticing what disappeared, and it seems like its only when you're a dretch right? I think it might be a funky vis problem. Check your portals in Radiant, maybe a stray structural or hint brush? Or with the odd angle of that section, maybe you need some hinting?
The way stuff disappears just reminds me of a tutorial I read about vis. There is some var where you can lock the vis and then travel around to see what disappeared around a corner. Also reminds me of r_showtris being on in game and seeing the wireframe disappear.