When an upgrade is performed to finalise installation for TimingAndEstimationPlugin, customized entries for TimingAndEstimationPlugin field labels are overwritten with default values.
This is a problem for people who are building new project wikis/repositories by script (and let's face it, the process is so involved setting up Trac/SVN with plugins, macros, customisations, etc, it HAS to be scripted). The setup script will tend to write to the INI file and then run the upgrade, you see. Of course, you can set the ini file afterwards, but not if TimingAndEstimation? is not enabled by default for all new wikis.
Upgrade process should probably detect that settings are already in place and leave them alone.