need your ship .entity and your model .mesh in txt mode ( not binary ) for find what is your problem...
Now, we can only make some guess... by example, your model is a capitalship with 3 weapons type in the entity file and in the .mesh you have hardpoint for weapons1, weapons2 and weapons3... wrong... hardpoint counting begin at 0, so you need weapons0, weapons1 and weapons2... since weapons0 have not hardpoint, it will be firing from the coordinate 0,0,0 ...
A advice, always use the dev.exe when you are modding... in the log, you can found what is wrong...
In short, show us your files and we will be able to help you...