I had a similar issue when deploying the software. The challenge is that the FaxFinder client does not appear to read the contents of the file during operation, only reads on opening and writes to on closing. I tried pushing the files out as read only to prevent the software from deleting my server configs on exit, but the client would crash as I recall when I did that.
My best solution was to create a script that would terminate the faxfinder process, overwrite the ini file with my copy, then relaunch the client. This was with an older version of the software, however, so things may have changed since then. I do know that when one of my team members was investigating it and called support, at that time there was no way to officially push out server configs, which is unfortunate as it would make deployment much easier, especially with the AD integration in the x40 line.