Some weird new bug I've detected:
With everything in the compile set to final compile (I always compile that way ). the hive in starboard generator (map=achio btw) is somehow pitch black, no light casted on it at all . I have tried moving it, deleting it and creating a brand new entity, but it refuses to be lit and stays pitchblack in a fully lit room...

Any ideas on this?

Remember that all models in HL get their lighting from the floor directly under them. I believe there were issues when you're trying to use a skybox to cast light on a model, making it pitch black. I guess you'll have to use a spotlight to illuminate it or something.