I think I found the issue after 2 weeks of pulling out my hair. For anyone experiencing this issue, hopefully this will save you the aggravation and time. In using phonegap builder, I've also enabled hydration which allows the app to pull in updates and 'self-update' without having to reinstall the apk or ipa file. I completely removed the app and reinstalled it manually without relying on hydration and it resolved all the issues. I think there is an issue with hydration in correctly updating the files and making changes to the actual files and it was causing unnecessary problems.