Does indeed sound like a Source engine error.

Oh well, I know you said prefab but are those tables and chairs your putting into the level models? I can't really remember any black flickering errors on bsp geometry in GoldSource. Unless your using a switchable texture, for some reason, a narrow array of textures (mainly that aren't used anyway) are switchable and appear as if there is a florescent light in the room, causing the textures to flicker darker and lighter. These textures where probably early textures made back when GoldSource didn't have any light entities.

Just try re-texturing that surface with say a concrete texture and see if it still does it.

It's in Half-Life 1.

First of all, this sounds like a common HL2 error. Is this for HL or HL2?

-If it is indeed for HL2, then the problem is the textures you chose to apply to the walls and ceiling. if the texture has the words: 'model' or 'prop' in its name or file path, then you most likely are using model textures for world brushes which only causes problems, because models use 'vertexlitgeneric' while brushes use lightmaps for lighting.

If this indeed is the error, then I would post a link to another thread where the problem was answered before. (But I can't find one atm.)

Solution: simply replace any textures that are blinking with any texture from hammer that doesn't have the word prop or model in its name or filepath.