I've noticed that whenever one reloads a save in X3: Terran Conflict that the control profile for the Xbox 360 controller will be wiped out for some reason. I'm using X3: Terran War Pack (Terran Conflict) v3.4 (17049) on Windows 7 64-bit. Because of this bug, the game becomes unplayable after a save is loaded. I've attached a screenshot before and after the save.

Does anyone know if this bug occurred in a previous version of X3: Terran Conflict?

That bug has been present for a long time in X3AP. I've noticed the same thing, can't remember if this fixes it, but AFAIK if you save the profile under a new name it might remember the custom bindings.