So, I'm working on my map this morning. I tweak some lights and such, compile and load the map in TF2... and it's awful. Everything in way, way too dark. So, I go back into Hammer... every thing that I func_detailed... is no longer func_detailed. I was irritiated, to say the least. So, I try to func_detail something as a test and and it won't stay tied to the entity. As soon as I click away and then back, it's no longer func_detailed.
Try switching between "groups" and "objects" by the buttons in the top right. I can't recall exactly how it works because I'm not in Hammer, but sometimes it doesn't recognize something as what it really is if you are in a different selection mode.
Does that make any sense? Try it and see if it helps.
Does your compile log say anything about having leaks? If your map has a leak, Vrad doesn't compute bounce light, and everything looks darker (especially ceilings). One cause for your leaks (if you have them) may actually be the func_details you've made. A func_detail can't plug a leak.