If your tests of "almost always" include shooting outside in good light, then if your camera is choosing ISO 3200 in Auto mode something very funny is going on. Either you've managed to set a strange option somewhere, or the camera itself is broken in some way - doing a factory reset would rule out the first option. That should be the first thing you test.
If your tests are all indoors, then ISO 3200 is probably quite a reasonable choice. I don't know the details of how Nikon cameras handle exposure when a flash is attached, but it's certainly the case that Canon cameras will in some modes use the flash only for fill, and still expose for the ambient light; if Nikons do something similar then it will make no difference if you have an external flash attached or not.
As has already been commented, if you want to have control over what your camera is doing, you need to get out of auto mode. This tends to be doubly true if you're using flash, when the whole question of using the flash as a fill light or a main light comes into play - you probably have some strong views on this (sounds like you want it to act as the main light in your case), but there's not necessarily any way of telling the camera what you want.