Yep!
I'm using MO and i just had the same issue and guess what: with the same mods!
English is not my native language so tell me if I misspelled.
Fore those you don't know Mod Organizer at all, otherwise ignore the first part:
Mod Organizer doesn't install the mod in the "Data" folder. It create a virtual "Data" folder to install your mods.
With MO, you can create several profiles with specifics "ini settings", mods construction.
You can also give priority to your mods without reinstall them every time.
Example: "NMC's textures pack" and "Poco Bueno". Let's say you want Poco Bueno to overwrite NMC's textures pack.
With Nexus Mod Manager or Fallout Mod Manager you will have to install NMC's first and Poco Bueno after it.
But if you want to switch to another texture pack or if you rather the NMC's textures pack over Poco Bueno, you'll have to remove them all and reinstall them again, right?
With MO, you just have to move your textures pack like you would do it for a plugin in your load order.
MO recreate the virtual "Data" folder every time you give a priority to a mod or another. With MO, the real "Data" folder stay untouched, just like a fresh install.
With NMM or FOMM, to install a mod over another one, you have to be sure because remove them and reinstall them again take times.
With MO, you only have to move a mod before or after another one just like for the load order, it's "much much much faster"
More information here: http://www.nexusmods.com/skyrim/mods/1334/? (MO Nexus page)
Here: http://wiki.step-project.com/Guide:Mod_Organizer (MO guide from STEP)
And here: http://wiki.step-project.com/User:EssArrBee/FalloutNewVegas (specific FNV guide, Last Update: 2 May 2014)
Now let's talk about your problem.
Obviously, those who are not familiar with MO, will still have some troubles to understand ;)
I suppose that you know essentials things like how to mod FNV, what is and how to handle your load order, etc..
I'm not sure about what could be the problem but i had this issue since i tried to add "JiP-CC&C".
JiP-CC&C work only with NVSE 4.2b4 so i installed it with this mod, i was using NVSE 3.2b4 before that and everything was fine. So i believed it was something about NVSE but i saw a weird thing with MO.
If you installed "Project Nevada", "oHUD" or any mod that modify the "hud_main_menu.xml" with MO (without FOMM), this important file just disappear from the "MO's mods folder".
It shouldn't but when you run "uHUD" (with FOMM through MO), it use this files to merge all of the "UI or HUD mods" : uHUD (FOMM through MO) doesn't make a copy of "hud_main_menu.xml", it just use it to create new files including of the "UI or HUD mods".
So what? The first time you will run "uHUD" with FOMM through MO it will works... (create a mod with the "overwrite" folder which contains the new UI / HUD files, created by "uHUD") ...but if you add more "UI or HUD mods" after you will have to run it again.
The second time you will run it, "uHUD" won't find all of the needed files because they being used the first time. (Project Nevada is the perfect example, if you want to recreate this)
Now if you install ALL of those mods with FOMM through MO, it will create a "new mod" in the "overwrite folder" with all of the needed files. (a fresh install)
You can't install those mods directly with MO, you really have to install them with FOMM through MO.
[quote="Groucho14E"] The particular combination of mods was TTWInteriors and/or JIP Companions Command & Control plus any of the following: Interior Lighting Overhaul, Flashlight NVSE, and Vault 22 Flora Overhaul. Deactivating one of them solved the problem. This was confusing as because FNVEdit didn't show any conflicts among them.[/quote]
To me everything was fine before adding "JiP-CC&C" but even after removed it I wasn't able to use Interior Lightning, Vault22 flora and TTW interior project together but no problem with Flashlight NVSE.
I tried several combinations by giving them much or less priority but no success. I think it's something related to MO, the way mods are install with it.
You can try to reinstall completely MO, backup your mods folder or ini setting is maybe not a good idea in this case. It would be better to reinstall your mods once again just like a fresh install.
Also, I'm not sure it's a good idea to extract all of the BSA (MO ask for it every time) when using TWW.
If you read all of this, i hope your eyes aren't to painful... ;)
Video games are bad for you? That's what they said about rock'n'roll...