There are a few situations where BatChmod cannot change the privileges of some files. For example, if a file is set as immutable, no one can modify it in any way, and BatChmod is no exception.
Also, if some files are locked and you do not select the Unlock option, BatChmod will not report any errors. This is due to the nature of the Unix commands that BatChmod uses, for which it is very complex to get feedback.
When applying privileges to files and folders, the Finder is not always updated right away. Although it should respect the new privileges, it may have the wrong icons and some privileges cached. Logging out and back in should resolve this.