The Aquarium Experiment: Hunchfish of Notre Dame

Hope he will not scare the other fish to instant death

 

Good luck!

Now I understand what you was meaning! You can fix that on Blender by rotating the bone that affect that vertex group, save the skeleton that you'll edit on Blender with a different name than the salmon one, when you'll introduce the Betta model on the CK you'll chose separately the skeleton that you previous edited to avoid any modification on the original salmon model (easy to do in complex);
You was trying to fix that on nifskope on the capsule rotation, now that I understand, I tryed that for my models too in the past, didn't work, nifskope on skeleton.nif files can only scale on axes x,y and z at the same time of a single bone or to all the bones apparatus, you can't rotate, move or scale the single bones on the single axes.
If you need a guide to how to fix that in Blender give a look here, bones basic transform functions work just like a normal vertex, edge or face edit functions (s for scaling the bone, r to rotate etc..).

At first, yesterday, I realized that the problem was inherent in the collision box on the salmon, collision box are a sort of interaction between the object or mesh that are assigned to the entire world behavior, but you don't need it, since your fish it's just like the bee in the glass jar of Skyrim, the jar have a collision box to interact with all the world, the bee inside no, infact you can't do anything with that and i don't think that there's some crazy guy out there that want to hit your Betta fish, at last if you want in future add a collision box to the betta that  can allow you to take directly the fish from the acquarium.
Apologize for the misunderstanding, but believe me, it's hard for me to translate and
correctly understand that form a shoutbox at about the 4:00 a.m.