Debugging in, I see that at SqlFileChange:143, my ChangeLogParameters are null, so there's nothing to do the property expansion with.
Here's the structure of my changelogs
update.xml
A property
include constants.xml <!--properties defined here. Some depend on property defined above-->
include v1_2_3.xml
include run_always.xml <!-- changes here used to see properties from constants.xml -->
I switch back to 3.1.1 and everything works as expected. I even mangled something to check for the false positive and the run_always that depends on a property in constants.xml fixed the mangled object.