Had you emptied the Save folder before beginning TMO_BH play sortofredhead? If you fail to empty the Save folder ("C:\Users \UserName \Documents \SH4" by default), or don't create a new, uniquely-named folder with
MultiSH4, then you end up with a mix of what you had before TMO_BH, and what you have now. Also, you should never attempt to use previous Saves after changing the overal mod load-out. It can be problematic even changing some of the seemingly simpler mods.
Also, there are some torpedo mods that are NOT compatible with TMO_BH, so if you have added a mod like that, try to remove it and see what happens.