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Does CatTools think that the config is a NEW config with each run, or is it telling you that the config has CHANGED?
If NEW, then it suggests that the original config file in the \Configs folder either:
a) doesn't exist
b) exists, but CatTools cannot access it to diff against the temp config file just pulled from the device; or
c) you have used a filename variable http://www.kiwisyslog.com/help/cattools/act_filenamevariables.htm - such as %DateISO% in the 'Current config file' field within the activity setup. This will effectively generate a different filename for every day you run the config backup activity. Because the filename variables values are determined at runtime; CatTools will then be looking for a file with the current date in the filename, however your backup on disk is named with yesterday's date. Because CatTools can't find the file, it therefore thinks that this must be the first time the device was backed up.
The other date/time filename variables will also cause similar issues as they change. Variables such as %BaseFile% are static in terms of the current device you are backing up, so do not have this issue.
If the issue is that the CatTools is always reporting config has changed, then you'll need to raise a support ticket so we can get some diagnostics and PuTTY captures from you.