Another issue that I am noticing with this trainer (64bit) is that if you are in a fight with enemies or pirates, make sure you disable 1, 2, 3, or 4. If you have infinite energy, there may be some instances where the enemy will have infinite shields or hull and not get destroyed. I am running Win 10 64 bit (Build 1511).
I'm having the same problem except I'm running Win 7 64 bit