If any of the program rules assigns the value of an TEI attribute to another it may be related to the other issue reported by the community.
If so it’s DHIS2 core related, happens on v40 and v41 (if they are using the new importer, which will be active by default if no ASWA is installed) and will be fixed in the next minor patch release. A way to verify this would be to create do a quick test with one of the program rules that don’t work in a 2.39 instance.