EDIT:

Can anyone explain this?

I replaced my fallout.ini file back to its original state and the game not only starts up fine (as expected) but all my mods are in and work perfectly fine?

. . Im confused, like I don't really know how that is possible?

for archive invalidation invalidated, u can rename it or move it so meshes.bsa and texture.bsa are after AII.
if u rename it, u could use Fallout - AII.bsa in the fallout_default.ini and the dummy file in the data folder
also, fake sure u have the latest version of new vegas script extender and fomm

Thanks

Using the load order tool and a bsa file and ini edit and no problems here.