This happened about half a year ago, and since then I've been extremely frustrated with search results online... So yay for a first post on ANY photography forum : P
I'm pretty sure this started after I was using a old manual lens from my dad's Nikon F104s, because about 3 hours into shooting the aperture just locked on me. I couldn't change it, but it would just fluctuate back and forth to the original number. Further testing showed that it did it with EVERYTHING the back wheel controlled (ie. shutter, iso). I've tried battery pulls, different SD cards, reflashing the firmware, and cleaning the contacts. I'm actually rather desperate now, has anybody figured out a fix for this, or should I throw in the towel and save up for an old D90?
Some things need to be cleared up, but if it's under warranty, do that.
First, did you only use a manual lens on the D3100? Because spinning the thumb wheel will do nothing for aperture and shutter speed on a manual lens. Other than mounting of the lens, the camera doesn't communicate with the lens, so you can't do exposure with it and you have to rely on the focus indicator in the viewfinder. In other words, you have to adjust the aperture with the ring on the lens.
This also means that you can't use the thumb dial on "S" mode with a manual lens.. the camera doesn't know the lens aperture and therefore can't calculate exposure. The only way you can use the lens is in "M" mode.
However... you should be able to control the ISO by the thumb wheel. If you dive into the menu and none of the dial selectable menu options respond, then there might be something wrong.