I can only assume, that something that the Dev's weren't allowed to release to us was removed before we got the new GECK and, it broke somethings unintentionally. There are other major GECK bugs such as, you can no longer duplicate worldspaces and, I hear but haven't tested the update faceGen no longer works properly.
It svcks but for now we have to find workarounds and, hope, pray for a GECK update which will fix these issues.
cev
There's definitely some other strange anomalies with the lighting as well. To me it seems that it just doesn't render the lighting like it did with the FO3 version. If I move a light bulb, as soon as I drag it it turns off, lol. It also makes for a real PITA trying to position your lighting. I've taken to the laborious procedure of placing a light in my mod, saving, loading the game and checking how it actually looks in game. Then trying to position it to get the desired effect. It's not too bad if you are using the same basic lights over and over, but if you're trying for subtle differences in lighting, it's a real pain, lol.
Is there something I'm missing with the lighting?
Oh, and not trying to be a sour puss, but I personally don't expect to see any updates to fix this stuff. They can't even get a patch out for the folks who are having trouble with the vanilla game, so sadly us modders are probably the lowest priority.