The ability to limit the differential diagnosis list by incubation period was added in 2012. There are seven options beginning with 0-6 hours and ending with >2 years. Infectious diseases have a range for the incubation, and I use the data in CCDM if available. For diptheria, it is 2-5 days, so both 24-48 hours and 2-14 days are checked. For botulism, it is 12-36 hours, but may be several days after eating contaminated food and 4-17 days after a wound infection, so 3 of the 7 options are checked.
Most infectious diseases have a range that encompasses more than one of the seven incubation periods in IDdx. One strategy would be to try your query with more than one period (Match Any or OR query) selected to see if this changes your results.