I would suggest checking the analysis logs to understand what analysis parameters are being taken into consideration.
[**INFO**] Project configuration:
[**INFO**] Excluded sources for coverage: **/*.java
You mentioned that the **/src/main/java/**/*DAO.* is set in the UI… if a developer, for example, added sonar.coverage.exclusions somewhere else (in the pom.xml, as an analysis parameter to mvn sonar:sonar), this would be overridden by the hierarchy of settings.