Twilight: not only that, it's a matter of how the game engine is loading information... it rewrites first loaded mods with later loaded mods, as long as they affect the same item/NPC/game setting. For example...
Mod 1 - unofficial patch (changes a million things around the game)
Mod 2 - a rebalancing mod (changes weapon statistics)
Mod 3 - mod changing the damage of gauss rifle
I wrote these mods in the correct order... first the patch fixes a problem with the gauss rifle, then the other mod balances it and the third mod is your personal preference to increase its damage.
In the opposite order, it would be a problem - first you change the damage like you want - then the damage gets overwritten with the balancing mod - and finally even the balancing mod will be overwritten with a patch. Item statistics and other things in-game are saved as a whole... if you change the damage of a weapon, the mod will also save information about everything else - ammo, weight, ...
This is how Gamebryo engine works since Morrowind and it's a very flexible system if you know how to use it :)
One more problem is, if Mod 2 is referencing Mod 1... if you load Mod 2 first, the game will simply crash.
Not to bash on mod developers, but that sounds like improper programming practices. Where they aren't testing to make sure that what they're monkeying around with is in a state to be adjusted. Not that that is particularly easy to do.