There are a two different reasons for this. 1) The feature does get installed after the configfile has been "edited" 2) The feature only contains a config section and not a configfile section
I'd guess reason one is the most likely cause of this since it needs a running Karaf to install a feature through Pax Exam. So to work around reason one, replace the config with a config file present in your test project. For reason two, make sure the feature actually does reference a config instead of a configuration admin config, or add your config to the configuration of the config-admin service. You can achieve this by injecting the ConfigAdmin service in your unit test and add your properties to the configuration pid.
EDIT: Combine both solutions Since because of 1) it takes longer for the config-file to be actually available, let config-admin service do the rest. Make sure your test does retrieve the config-admin service either by injecting it or by waiting for it's availability. Now within a @Before method make sure you wait till your config is complete and change it from there on. This way you don't need to duplicate the config files.