Objects (mostly Raven Rock) from Bloodmoon.esm have their location changed in wl_SolstheimOverhaul_v1.esm to accommodate the new and improved landscape. The OpenCS shows everything correctly, but in-game everything appears in their original position, that is below land. Even without other mods loaded the issue persists, so I think it's OpenMW.
http://imgur.com/a/lHwWF
1 - Above Land, floating windows = new references
2 & 3 - Below Land, old references in original positions
Mod in question:
http://www.nexusmods.com/morrowind/mods/42979/?