If your grates are properly sealed, the next big question is how is your draft measurement. If it is too high, the draft will pull air through the hopper and the fire will follow the new source of air flow. Koker's draft should be .02 - .03, .025 being ideal. Take a look at Keystoker's web site, they have new versions of their stove's manuals and they are easier to understand. If you don't have a monometer, make it priority 1 and get one. This may eliminate your problem, and will also save you on fuel costs as high drafts just suck the heat right out of your stove rather than having the heat waiting to transfer into your house.
Oh, Keystoker also suggests keeping your coal hopper full, again making it hard for air to filter through the coal.