OK, I've had an extremely stressful evening.
I made a sim me in BodyShop. For the benefit of the MATY downloaders, I moved her into an empty lot and played the game for 1 sim minute. Then I edited her job, interests and skill levels to be "correct", and packaged the lot. This is safe, because she hasn't met anyone at all, so can't possibly take any "ghost" (unlinked) copies of all the sims she ever knew, as that's no one. The contents of the .sims2pack are simply: a lotSegmentForUpload, a familySegmentForUpload, sim me, and sim me's everyday outfit.
To cut a very long story short, while CleanInstaller lists the contents of the .sims2pack correctly, it doesn't install the package properly. When the lot installs, it's an empty lot containing The Baratron Family, which is apparently 8 non-existent empty sims, all called SimName Moniker. WTF? I tried a whole bunch of things to fix it, right up to removing my entire Sims 2 folder and letting the game regenerate it. But the only thing that actually worked was... not letting CleanInstaller install the file, and instead forcing it to be Opened with the game's own installer! This has happily unpacked the occupied file with sim me intact!
Has anyone else had this problem before? I've never tried to package an occupied lot before because we all know that occupado = bad. But I thought CleanInstaller worked!