Not sure about wakeboard bindings but I had some soccer cleats I bought used that had a nasty smell on them even after being in the washer that would stick to my feet and fingers when putting them on. I took a can of axe and sprayed a little inside and blow dryed them with a blowdryer; I cant smell anything on them now! You might be able to try that, not sure if it would damage your bindings though
you could try using a disinfectant to soak it, it'd get rid of the smell if it's bacterial related.
get something like Dettol, dilute it to 10 parts water, soak the boots for 10mins, rinse a few times to get rid of the dettol smell and you should be alright.
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