Did you download and install ALL the mods that are required to make the Stargate ship pack work properly?
Also, you don't actually need to do anything with BCUT in order to get the stargate ships in-game. You just need the Foundation mod that comes with BCUT. Foundation makes BC 'mod friendly'.
The following is required to make the Stargate ship pack run properly, in this order:
BC official 1.1 patch
Foundation (comes with BCUT)
MVAM Infinite
Foundation Technologies
NanoFX 2
F_MineAI.py (if you dont want to install KM1, I have included F_MineAI.py in its own folder.
http://www.filefront.com/15709555/Open-me.zip/ )
I suggest that you make at least 2 installs of BC in seperate locations on your harddrive so that you can always revert to a basic install of the game if something goes wrong.
IMHO, it is always best to install script based mods first.