There is a bug (I think) with on-screen entities and skycubes. They do not appear when I define them, I have to 'ent_morph' each one in order for them to appear.
Sorry, but I can not tell from this sober report what the reason for your problem might be. My guess is that when there's a problem that only you have, but no one else, it's likely a bug in your code and not in the engine. Of course, this is only an assumption.