I was successful in removing odor from winter boots using baking soda. I just put the dust inside, and wore them normally.
The small drawback is that the socks might get whitey - the soda getting attached to them. Remove the soda from the socks by shaking or washing.
In your case, if the smell goes deep into the fabric of the shoes, you may need to actually wash the shoes again, using a (concentrated) solution of baking soda. This will allow the baking soda to go all the important places, and destroy the smell-making micro-organisms.
Here I wrote an answer, providing links about the baking soda being a good odor remover. You can actually use the baking soda on your body, and your sweat will not be scent-y (I do it myself, after other people told me about it).
I tried using off-the-shelf sprays for deodorizing the insides of shoes, and in my experience the effect was mostly "placebo". They seem to only add some scent to the stink When the scent goes, the stink is still there.