What could make a baby's cough sound croupy (that isn't croup) only lasting an hour or so. Dry throat? Second time toddler woke w scary cough. 

Sounds like croup. Croup is a barking (croupy) cough that is often worse at night (not all the time, necessarily). Mild croup is a viral illness that lasts for 4-7 days and is typically more distressing than serious. Look for signs that your kiddo is having trouble breathing as that means you may need to get them to the er right away.
Could be asthma. A young child that is awakening at night because of cough or difficulty breathing should be evaluated for asthma. Associated concerns would include a family history of eczema, allergies, or asthma, smoking in the home, premature delivery or prior lung infections such as RSV or several infections with "croup, " which as you have suggested should only occur once.