I recently updated NMM and my mods are now FUBAR and Skyrim is now giving me CTD's at start up. To try to fix the mess I downloaded and installed Mod Organizer to re-install my mods. LOOT in MO isn't reporting any conflicts but I'm still getting the CTD issue. Tried BOSS, BOSS said to run LOOT, so I DL and installed the current stand alone version. The stand alone LOOT reports 1 error:

"BBLS_PatioFurniture.esm

The SummerWear.esm file IS checked as active in Mod Organizer which I used to install it, and is present at C:\Program Files (x86)\Steam\steamapps\common\skyrim\Mod Organizer\mods\Summer Wear V2 nsfw\SummerWear.esm

Any idea why LOOT isn't seeing this one .esm file when it is seeing the rest of them? And is there any way to fix that issue?

Thanks
- Geoff

The "Sort" button inside of MO makes use of LOOT's API to sort the plugins; this works, but using it this way you will not be presented with LOOT's GUI (graphical user interface). The only way to see that is to always start the fully installed LOOT through MO.

Can you please post the content of your plugins.txt file from the following folder: ..\Mod Organizer\profiles\\..

Another advice I would give is to always install Steam/Skyrim, LOOT and Mod Organizer (or any other mod manager) outside of C:\Program Files or C:\Program Files (x86). These folders are influenced by https://en.wikipedia.org/wiki/User_Account_Control, which can lead to issues with one or more of the earlier mentioned tools/programs.

In any case, a CTD at start up is 99% of the time a direct result of a missing master plugin, which means, that you have at least one plugin in your load order, that has another plugin as a master - but that one is missing. Without said master plugin activated in your load order, the game will not start, and CTD. In your case this seems to be indeed SummerWear.esm. What happens, if your load your entire load order in TES5Edit? See https://www.youtube.com/watch?v=cPwiY7NBVTM video for explanations.