There are no configuration changes, the only difference is the JaCoCo version. Here are the detailed steps of what I am doing, it might be this sequence of steps that this issue occurs.
1. Execute my java unit and integration tests via maven using jacoco-maven-plugin
2. jacoco-ut.exec and jacoco-it.exec files generated for all the different projects
3. Merge all the .exec files into one file using jacoco-maven-plugin
4. Generate coverage html report on the merged .exec file using the jacoco Ant report task