Walls and objects are usually missing in random cells, this seems to be linked to any mod that changes locations, though no mod is responsible, just seems to happen if you have a lot of mods that change locations. Does anyone know a fix to this? I'd like to be able to play my Skyrim with more new buildings and land.

Posted about this a few days ago, http://www.gamesas.com/topic/1369525-cell-not-properly-loading/. Noone seems to know.
Maybe I am imagining but the game seems to have fixed this issue and became more stable after I played around with my RAM timings. Also be careful with many mods being in combination, that also adds to it I think. For now all you can really do is save immediately when you come into contact with the glitch (preferably new save), quit the game and reload; the cell should properly load now. After the 1.5 patch the game has been pretty botched for me; but like I said seems to be resolved after I timed my RAM a bit better.