The only thing I can think of is that there might be some sort of permissions issue either on your Library/Preferences folder or on the actual plist file.

In your home folder's Library/Preferences sub-folder there should be a file named: com.2manyrobots.Yate.plist

ie: ~/Library/Preferences/com.2manyrobots.Yate.plist

Open Yate and make a change to the preferences. Close Yate. The modification date/time of the above file should reflect the current time.

If the date/time does not look current make a copy of the file and then delete the original. Restart Yate and make some preference changes and then close Yate. Check the date of the newly constructed file.This may or may not work if you're on Mavericks or Yosemite as they do some pretty heavy caching of preference files. If you still do not have a working preference file you should try fixing your permissions. In fact, if this fixes the issue I would still repair the permissions.

If you look in the forum under Mac OS X issues there is a topic called 'Cocoa Error 13'. The post describes how to reset your home folder permissions. Since Lion, Disk Utility does not repair home folder permissions.

Make sure you keep the exported plist you used before.