The values defined in the web.xml file will always override the values you have modified with the admin console or by script. Solutions are :
Remove the values from the web.xml file. The first time you deploy the application you need to set the values. But after that when updating the application, all the values will not be overridden.
Leave the values in the web.xml and deploy by script (and not by the admin console). Here you can set the values when deploying the application with the -MapEnvEntryForWebMod option.