After thrashing it for 100s of hours on PS3 I have just start recently bought skyrim on PC to mod (late to the party I know).
I have used NMM for FONV and never had a problem there, however I seem to have problem after problem with skyrim.
With NV I didn't mod it too heavily so I never had a problem with load order however with skyrim I had over 100 mods that I wanted to try and the order wasn't right so it kept crashing. Because of this I tried not using so many mods. It wasnt too bad until I realised that skyrim wasnt recognising that I had SKSE installed. I reinstalled another few times but to no avail.
Next I tried using steam modding... I quickly realised that the options were much more limited there and when you are investing 100s of hours into a character you want to be able to use decent armour/weapons packs. So I tried using boss and TES5edit, TES5edit was only picking up my steam mods so I deleted skyrim and its mods on steam.
Now I have decided to try copy some the mods that gopher uses in his latest lets play series, I thought that would be safe. I had reinstalled skyrim, skse and each mod that I wanted to use (each with a clean install).
I am able to play with SKSE with no problem but the mods/plugins arent getting picked up by either the NMM or skyrim or getting lost on one of the cogs inbetween.
Some things worth noting:
-The plugins.txt (C:/Users/Admin/AppData/Local/Skyrim) has all the plugins listed that are selected in the NMM
-TES5Edit has in its log "Note: Active plugin List contains nonexistent file "ClimatesofTamriel.esm"" For each mod.
I am sure this is human error, but I cant find anyone that is having the same problem, maybe there is no one as special as me, but if you can see where I f***ed up can you let me know?