This isn't intuitive but goto Project Properties, make sure your transitions and photos are set for what you want, 2 seconds and 4 seconds for stills, for instance.
Then goto File-> Project Theme, reselect your theme and check automatically add transitions and themes, it resets the whole project correctly.
Thank you, beekayApple! Your solution was the only one that worked for me. For any others who try it, I ended up having to remove my transitions and add them back in again after reselecting, but Project Theme was definitely the key--I selected a different theme and then went back to my original theme and "bingo!" Thanks!