I found that the booties have got a lot of moisture trapped in them - even after letting them dry for several days - they are still wet. And if they are wet - and humid - mould, fungus, and bacteria will start to form - and they will stink.
One great way is to place old black/white newspaper (not glossy paper) - into the boot after you've dried them for awhile. And when you dry the boots - don't put them out in the sun (for too long) - because direct sunlight will damage the rubber.
The old newspaper will help to absorb the moisture in the booties. Pull it out the next day - and you'll find its damp. Throw it away and put in another one. Repeat until the newspaper is dry.
Then to store = I'd put in a 3rd set of "fresh" old newspapers - and throw in some cheap sodium bi-carb powder too - great stuff.
Its worth doing - if not, the bad smell in your booties will transfer the bacteria and germs to your feet the next time you put them on.