My assumption is that your situation is explained if you are using camera Auto mode. Your desire for low ISO will need to turn Auto ISO off with flash. However, if you are in camera Auto mode, you cannot turn Auto ISO off, so you have to get out of Auto mode, because, well, because Auto is automatic... auto ISO, auto White Balance, auto everything in Auto mode. That is its purpose.

The camera menu called Auto ISO is for camera A, S, P, or M modes (see the manual). But in Auto mode, everything is Auto, including ISO and WB, etc.

So you might have set ISO 100, and that does work in camera A, S, P, or M modes, but if you watch it, ISO will vary in Auto mode, and then ISO will be high indoors where you need flash, regardless if flash is used or not.

Nikon iTTL DSLRs have had three ways Auto ISO worked with flash. Cameras of the D3100 era are the middle way, and they increase Auto ISO for the ambient, regardless if flash is used or not (more detail on models at http://www.scantips.com/lights/flashbasics4b.html#iso2 .) Of course, Auto mode uses Auto ISO. So that means flash indoors will always be seeing high ISO if in Auto mode. You need to turn Auto ISO off for flash, which means you have have to get out of Auto mode if you want low ISO.

The earlier iTTL DSLR models did not do Auto ISO for flash, and the latest models have corrected it again, but the several models in the D3100 era sets Auto ISO determined only by ambient, regardless if flash is used or not. The Exif will show the ISO value it actually used with flash. You can turn Auto ISO off in camera modes A, S, P, or M. Or, if you put the flash into its Manual flash mode, ISO should always remain at minimum (manual flash cannot react to Auto ISO).

So you can use camera A or P mode, and set any ISO, and a reasonable aperture, and TTL will take care of the flash. The shutter speed will likely always be 1/60 second with flash. And you may want to set White Balance and Picture Control, because these are not necessarily auto in modes A, S, P, or M.