If you can post your MO logs please so we can examine them. Also your modlist.txt will help determine which mods might be misplaced.
here is mo log or at least what i think you meant by mo log
06:54:28 [D] Working directory: D:\steam&maybe other game stuff\steamapps\common\Skyrim\Mod Organizer\stylesheets
06:54:28 [D] MO at: D:\steam&maybe other game stuff\steamapps\common\Skyrim\Mod Organizer
06:54:28 [D] initializing core
06:54:28 [D] initialize plugins
06:54:28 [D] looking for plugins in D:\steam&maybe other game stuff\steamapps\common\Skyrim\Mod Organizer\plugins
06:54:28 [D] loaded plugin "bsaExtractor.dll"
06:54:28 [D] loaded plugin "checkFNIS.dll"
06:54:28 [D] loaded plugin "diagnoseBasic.dll"
06:54:28 [D] loaded plugin "gameFallout3.dll"
06:54:28 [D] loaded plugin "gameFalloutNV.dll"
06:54:28 [D] loaded plugin "gameOblivion.dll"
06:54:28 [D] loaded plugin "gameSkyrim.dll"
06:54:28 [D] loaded plugin "iniEditor.dll"
06:54:28 [D] loaded plugin "installerBAIN.dll"
06:54:28 [D] loaded plugin "installerBundle.dll"
06:54:28 [D] loaded plugin "installerFomod.dll"
06:54:28 [D] loaded plugin "installerManual.dll"
06:54:28 [D] loaded plugin "installerNCC.dll"
06:54:28 [D] loaded plugin "installerQuick.dll"
06:54:28 [D] loaded plugin "NMMImport.dll"
06:54:28 [D] loaded plugin "previewBase.dll"
06:54:28 [D] loaded plugin "pyCfg.py"
06:54:28 [D] loaded plugin "proxyPython.dll"
06:54:28 [D] downloads after refresh: 39
06:54:28 [D] game path: D:\steam&maybe other game stuff\steamapps\common\Skyrim
06:54:28 [D] managing game at D:\steam&maybe other game stuff\steamapps\common\Skyrim
06:54:28 [D] setting up configured executables
06:54:28 [D] configured profile: solo game
06:54:28 [D] D:\steam&maybe other game stuff\steamapps\common\Skyrim\Mod Organizer\profiles\solo game\modlist.txt saved
06:54:28 [D] validating login cookies
06:54:28 [D] initializing tutorials
06:54:28 [D] loaded language en-US
06:54:29 [D] interface Wi-Fi seems to be up (address: fe80::f45b:e2b4:5600:5092%4)
06:54:29 [D] displaying main window
06:54:29 [D] retrieving credentials
06:54:29 [D] user is premium
06:55:28 [D] D:\steam&maybe other game stuff\steamapps\common\Skyrim\Mod Organizer\profiles\solo game\initweaks.ini saved
06:55:28 [D] D:\steam&maybe other game stuff\steamapps\common\Skyrim\Mod Organizer\profiles\solo game\plugins.txt saved
06:55:28 [D] D:\steam&maybe other game stuff\steamapps\common\Skyrim\Mod Organizer\profiles\solo game\loadorder.txt saved
06:55:28 [D] D:\steam&maybe other game stuff\steamapps\common\Skyrim\Mod Organizer\profiles\solo game\lockedorder.txt saved
06:55:29 [D] D:\steam&maybe other game stuff\steamapps\common\Skyrim\Mod Organizer\profiles\solo game\archives.txt saved
06:55:55 [D] D:\steam&maybe other game stuff\steamapps\common\Skyrim\Mod Organizer\profiles\solo game\initweaks.ini saved
06:55:55 [D] D:\steam&maybe other game stuff\steamapps\common\Skyrim\Mod Organizer\profiles\solo game\lockedorder.txt saved
[]
where is the modlist.txt or if this log i posted is it where is the mo logs