You probably re-writing the values in Local Storage before the loader layout is complete. Don't write to Local Storage on every second! Only write when something important has changed (level finished, upgrade purchased etc.)
Local Storage operations are not instant, they may take a few ticks to finish. So you should never allow a situation when you "get" and "set" values in local storage at the same time.
Right now you can add "Local storage clear" to the project and run it once to get rid of "NaN" values.