The bug seems to be this: loose non-static items get havoked when the cell they are contained in is loaded. Normally this is no problem, though poorly placed items can sometimes move around. But if the item is placed near a cell border, and if the item havoks its way across the cell border into an as-yet-unloaded neighboring cell, the contents of the neighboring cell will never load.
What led me to discover this was that when the bug occurred with Fort Magia, there was a set of three loose items stacked floating in the air in front of the fort door ( picture http://i86.photobucket.com/albums/k90/in_a_coma_dial_999/Oblivion/before1.jpg ) and a few items right on the border with the neighboring cell. Those items are normally located inside a small ruined tower ( CS pic http://i86.photobucket.com/albums/k90/in_a_coma_dial_999/Oblivion/before0.jpg ). Looking in the CS, I noticed that the border between the Fort Magia exterior cell and its neighboring cell passes right through the center of that tower ( picture http://i86.photobucket.com/albums/k90/in_a_coma_dial_999/Oblivion/cellborder.jpg ). And the items that were floating in front of the Fort Magia door were all ones placed in the neighboring cell, not in the Fort Magia cell itself.
I "fixed" the problem in the CS by moving all of the items into the Fort Magia cell, but still in the little tower ( pic http://i86.photobucket.com/albums/k90/in_a_coma_dial_999/Oblivion/after0.jpg ). That prevents the problem occurring, because the offending items don't get loaded until the cell containing the Fort gets loaded. But... yup, you guessed it: if I approach the area from across the water, the opposite problem can occur, and the cell next to Fort Magia can now fail to load, leaving a big hole there instead.
I decided to make a more general test. I made a trivial mod that places a big rock in Wilderness (17,13) right on the border with (16,13) such that part of the rock extends into (16,13). Then I placed a skull in (16,13) that sits on the protruding part of the rock. Sure enough, if I approach the area from the (16,13) side, the skull rolls into (17,13) and there's a big square hole in the ground. So the problem is definitely reproducible.
My suspicion is that the items getting havoked into a neighboring cell causes the game engine to mark that cell's contents as already loaded. So, when the player moves closer to the cell, the engine doesn't draw the cell contents because it thinks it doesn't need to. There is also some interaction with mods in all of this; it only seems to happen when a mod edits the contents of a cell. I also noticed that any items that are modified by the mod do get drawn -- you'll notice in the pic I linked above that there are a couple of rocks and a tree in the otherwise empty Fort Magia cell -- those items are the ones that the UOP moves. Everything the UOP doesn't touch, doesn't get drawn.
Anyway, I thought I'd share, as I think this may explain some of the weird missing-landscape issues that plague certain areas in the game when mods make changes to cells in those areas.