are you talking about your new water has a funny smell to it? ive had that happen when i kept new water in buckets waiting to use it (gets a fishy smell). I think its from just sitting there not moving. try adding an airstone for a day to see if that helps. will also help oxygenate the water before you add it to your tank which is a good thing (necessary) as well. let me know if I misunderstood you.
if the stinky water is in your display tank, you may have had something die. better find it. also, run carbon; that will help remove impurities and junk out of the water too and help with the smell (and any discoloring of the water).