As a fellow keeper of geckos that eat CGD, here's what has worked for me:
First, get rid of any foods that are sitting around, including dirty dishes in the sink.
Put some fly paper up near your gecko cages.
Next, count on leaving any cup of CGD in the gecko's tank for no longer than 2 days. After 2 days, you're not going to throw it in the garbage can--instead, seal it in a ziplock bag, or throw it in a trash can OUTSIDE of your home. They will happily breed in the CGD, and that is probably what is happening.
If you can keep all of this up for a month, including keeping the gecko cages nicely cleaned (in case they're breeding in the gecko droppings as well), the flies should disappear. We are currently fruit-fly free (except for the flightless ones that I culture), so it worked, here.
Just remember--if fruit flies can breed in it, it goes outside, rather than in the household trash. The key to them is identifying the source. If you throw away anything with larvae, you'll have no more flies. Once they're gone, they'll stay gone...at least, until summer.
By the way, if you see very slightly larger, darker colored flies with hunchbacks, those aren't fruit flies, but instead are phorid flies. Phorid flies will feed on droppings, meat, any sort of random food stuff, so can be even more of a nuisance than the fruit flies. Get rid of them the same way, by removing anything they might breed in before they have a chance to complete their lifecycle.