How do I get the smell of burnt food off of the inside of my microwave oven?
Working in restaurants similar things to this happened a lot. Our quick fix that usually did the trick was 50/50 vinegar and water and boil it off as mentioned above. Lemon juice or even orange should work instead of vinegar for a better scent.
At a guess, the more acidy fluids help break down any splatter that may have gone into the vents.

Hint: this is also great to do just before cleaning the microwave, even baked on splatter comes off easily after the steam.