Both my friend and I play Skyrim. I found Skyrim Nexus and told him about it and gave him copies of the mods that I'd downloaded as well as NMM. I have a desktop running Windows 7 home edition and he has an Alienware laptop with Windows 7 Home. As far as hardware goes, there isn't a great deal of difference between them.

Using Vanilla install, it runs fine and mods such as Totally nvde, A Quality World Map and some others work fine on his laptop.

All the mods work on my copy of Skyrim but only some work on his.
Black_Tower_-_Black_Sacrament_Armor_V3-1a_NMM_INSTALL_ONLY-5696 (this is an awesome mod that I'd recommend to anyone by the way, the Nightingale armor retex for this is fantastic).
Sunnie_NG_Set_v1_1-5247-1-1
Both allow crafting of the Nightingale armor refuse to work on his computer but they both work fine on mine and I even have the suite in the Black Tower and have crafted all the different Black Sacrament armor sets. I even tried re-installing the game on his and added the updates I have on mine to make sure his game version was exactly the same as mine. That didn't work.

As a last resort, I copied all of the data files, (those that had been changed and those that had been added on my PC), into his installed game directory. Still no luck, the mods still refuse to work. This wasn't a merge or change to existing files, it was a direct overwrite so there is no reason on earth that it should have failed... But it did! I did notice that Riverwood Folly disappeared from his map and didn't even show up as an icon on the compass when he got near it. However, the Black Tower just wasn't there.

I eventually uninstalled his AV to make sure that wasn't interfering. Nope, that didn't work either.

I am now completely stumped. I have literally tried everything I know and yet his laptop still refuses to run those mods while mine happily runs them.

He put the "totally nvde" patch in for a laugh and it works fine but I do notice it's hard to get rid of on both our machines. Even installing the body mod with the nevernvde option doesn't seem to get rid of the nvde bodies.

Anyone else got any clues as to why two systems running the same OS and same version of Skyrim have different reactions to some mods.
We both have Administrator logins to prevent the usual "you must have admin rights to do this" error.

May want to check NMM setups and make sure the same .ESP files are loaded on both machines, including load ORDER. Could also be a savegame problem. Did you try swapping out saves?

Edit: One other thing comes to mind: is Skyrim the same version on both machines?

Learn how to use Wyre Bash and BAIN, then teach your friend how to use Wrye Bash and BAIN.
BAIN gives a user control of what does get overwritten, and prevents many of the problems you are describing.
Are you using BOSS to sort Your friends and Your own Load Orders? I think that just swapping the Data Folder from one PC to another does not work unless some other files are also swapped between the two computers.
I do a swap of mods between two different PC's all of the time, but both PC's use the Skyrim Mods Folder from my newer PC.

Skyrim Seeker:
We tried several save games to no avail. As I said above, I reinstalled his game and added the same updates to ensure he had the same version as me.

bradleyh:
I have a program that tracks changes made to files and additions to given folders. Absolutely anything that was changed in the game directory and sub-directories by the mods, even any EXE's and DLL's was copied and ported over.
After installing Skyrim fresh with the same updates I had, we tried just adding the Black Tower mod only. It just seems to reject that mod on his Laptop.

Last night, I went over the specs of his laptop more closely. Apart from his having a mobile version of the processor, our processors are the same. The only major difference I can see is that he has 4gb but I have 16gb RAM. I'm beginning to wonder if physical ram would play a part in this.

Now I am getting really angry with it.

We upgraded my friends laptop from 4gb to 8gb and tried again. His specs are exactly the same as mine now with the only difference that he's running an Alienware Laptop and I am running my own custom built PC.

Even removing all save games along with the skyrimprefs that are stored there, uninstalling Skyrim completely and NMM and starting fresh with the Black Tower mod installed only.

He started a new character and got to Riverwood to find... No Black Tower
This is really starting to become a saga.

Can someone give any clues as to possible causes?