I was having the same problem with a sword I converted from an Oblivion mod. To test it, I simply overwrote the SteelGreatsword.nif to see if it worked in game. When the game loaded, my companion was carrying my Skyforge Steel Greatsword, which was replaced by the new model. When I took it from her inventory, it appeared as the regular sword in both my hand and my inventory. Then it occurred to me that Bethesda used 1stPerson nifs for weapons and items that appear close up in 1st person view in Fallout 3. That way, they can have a lower quality texture on the 3rd person version and no one really notices. So, I found the 1stPersonSteelGreatsword.nif in the BSA and using the Nifskope method mentioned at the beginning of this post, I overwrote that one with my new nif and the weapon appeared correctly in menu and hands. Hope that helps.