ok here is the possible solution. I've done this myself. This is one of the 'first bone' type problems. No amount of scripting will fix it, it never did on the bipeds sinking and it wont for this as well.
1. Import a biped skeleton that has the first group of bones at x,y,z, 0,0,0,. The one from the boards will do fine.
2. select all the bones EXCEPT the ones between the feet. Delete them.
3. 'merge' your fish .ms3d (the one at the propper height) file with it. this will change the amount of animation frames to the amount in your fish as well as have the propper animation.
4. export with jt exporter.
The reason this works is because in the bone order you have put the first placed bone (from the biped) ,before the skeleton of the fish. This is a good way to import models that arent FPSC ready.
Hope that helps.
