You should delete the file
/My Documents/Run.GPS/configuration.xml
By doing this you will lose other settings too.
You can also edit the file and change False to True in this line:
<useHardwareKeys>True</useHardwareKeys>
I'm running Run.GPS 2.0.6 on my Samsung Smartphone. I accidently unchecked use hardware keys in the configuration and now I've lost the abiltly to use the application. I've tried uninstalling/resinstalling without success. How can I reset this configuration?