Please log out and re-login to the TimeTracker Web, Mobile, or Google Chrome apps if you have logged in before making the configuration changes. The configuration changes reflect only if you log out and re-login to the Time Tracker application.
If you are using the Time Tracker application within Salesforce, please make sure that you close all the tabs, (if you have opened Salesforce in multiple tabs) then log out of Salesforce and re-login to the Salesforce application to see the configuration changes.
e.g: If the configuration was set to track time for Projects and Task earlier and if you make the configuration changes to track time to Projects and Cases. Then you should log out of the application and re-login to see those changes in the app for tracking time.