If I understand you right, you move your models and your collisions do not move with them. Is this right?

Which is your approach to make your ships moving?

So you move them yourself by rotating and moving them, then drawing them and "hoping Newton will do the same"?

Or do you let Newton do the work and physics and just use the Newton matrices to draw your models?

In the second approch, everything should work fine if you use the Newtonbodys matrices.

In the first approach you need to set the changed matrices to the Newtonbodys by calling NewtonBodySetMatrix.

It's a little hard to help here with no insight of what you are doing...