I don't know much about that software but certain software also have an update service associated with an application. Can you check the services to see if there is an IBM update service for example? If there's one, i recommend stopping and disabling the service while provisioning the application.
If you have UEM/DEM maybe you could enforce disabling auto update.
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Could it be that you have a writable volume attached where this setting is different? If so it will overwrite the information within the appstack. Maybe a different appstack attached with the exact same setting??