Creating WAR using gradle bootWar target changes the checksum of flyway DB scripts

I am facing one strange issue while creating executable WAR using gradle plugin in spring boot application, flyway migration behaving strangely, it detects different check sum between eclipse run and executable WAR run.
I have checked same scenario using one demo application with same scripts in MAVEN, and it works just fine.
Can anyone help me out here ? what is going on with bootWar target that flyway detects different checksum then applied by eclipse run previously.