The repository index for XYZ does not match the repository configuration - using configuration from current index
The following warning appears in the Fisheye log files:
2013-03-08 03:09:00,228 WARN - The repository index for "XYZ" does not match the repository configuration - using configuration from current index
This means that the current index on disk for the XYZ repository does not match the configuration in the config.xml for that repository. For example, diffText and LOC enabled may be different.
Either doing a re-index of that repository, or toggling those values back to how they were when the repository was first created will make this warning go away. It is not essential however.