Is your sand staying dry, or is it damp? And how is the ventilation in your coop?
The main idea is to keep things as dry and well ventilated as possible. One of the main reasons folks like to use sand is that If it gets wet, it will dry out faster than just about any other coop/run flooring/bedding material (e.g. wood chips, straw, dirt, etc.), and won't rot/decompose (although wet poop and/or food in the sand can still do so).
But even with sand, you will also need good drainage and ventilation to let any accumulated moisture run out or evaporate. So if your coop/run is trapping moisture in, you may have a problem. Make sure you have good drainage, and keep windows / etc. as wide-open as you can, weather permitting.
Finally, there will always be a little bit of "smell" involved w/ keeping livestock -- it can be kept down, but think that it's somewhat unrealistic to expect to eliminate in entirely. Really strong odors / ammonia / lots of flies / etc. indicate that you've got a problem that needs attention. But a little bit of mild "animal" scent is par for the course.