This seems to be an issue with the query we use to check for changes. It seems to be picking up on all sorts of system objects that it should really filter out.
We have had this and a few other problems with the 3.1 release, so we've actually now pulled it from the website until we fix these issues with the shared model.
I would recommend downgrading to version 3.0 for the time being:
http://downloads.red-gate.com/checkforu ... 3.4214.exe
Sorry for the inconvenience.