I have tried everything [well almost everything] to get the buildings and other objects to show up in Balmora in the CK [only a few HH doors show] and some other places have the same problem,but most of it is fine in the game.
If I remember correctly some towns [cell blocks] had thier own WRLD in the old morrowind CS,and am thinking that those CELLS were not converted over with the rest of wrld_morrowind by the converter.
If not then it is going to be real hard to add and edit detail in those regions.?

Did Morroblivion have this same issue? Or was everything converted over properly for them?
Good point Mehh,not sure,but I don`t think that the oblivion CS gives any WRLD errors like we are getting.
Will check it out though,because it might be possible to dump some data from morroblivion,and port it across using hex editing or something.
but even without checking I know that Balmora and other places are ok in the CS for morroblivion,because I placed stuff in there when writing some mods.
i had the same problem when loading both skyrim.esm and morrowind_sk.esm in the cs, and if you check editorwarnings.txt you can see many errors like:
DEFAULT: OUT OF HANDLE ARRAY ENTRIES. Null handle created for pointer 3bea87c8.
so ck just deletes the meshes/entries for some strange reason
but if you only load morrowind esm file everything is ok.
I guess we have to fix the numerous errors in the morrowind.esm file first, there are thousands of them,
Yes eloth,our morrowind_sk master is certainly a mess.looks look I will be making TESVEdit and other tools red hot with over use for a long time,but it will be worth it.
The master download will stay at v_10a for a while I guess,but making some prgress.
most problems are related to landscape, and landscape textures, if i go to a problematic cell, and repaint the landscape, the problem goes away.
To identify problem cells, you can see both purple ground(broken texture link), and flickering landscape when rotating camera in CK. so there are two main problems, the purple ground is easily fixed, the broken texture link must be redirected to txUglUdirtU01, like in morrowind(in morrowind two landtexture ID`s used the same texture, so i guess the converter got confused about that)