What file types (extensions) are your config files? Also, what triggers the repair? Do you get this repair prompt as soon as you launch your application? If so, does it act differently if you launch it from a shortcut or run it directly?
In general, I recommend having your application generate a default config file instead of installing one. This would be one solution to your problem, as the installer would not know or care about the file. Your application just has to look for a config file to use, and if one is not found, it writes a default file to disk and uses that.
Mert A.
National Instruments