In case this was not you, who I have wrote an email on same issue today, I will explain here.
CompareIt compares pdf files by extracting text from it. Unfortunately, some pdf files just can not be processed in this was - since it can be created so it will include image with text on it, not just text.
On other hand, some new pdf files are not processed by pdf library we use. In our recent beta (http://www.grigsoft.com/wincmp4bu.zip
) we have alternative pdf library. To use it, get this version, open files with it, and switch to View>ViewAs>MSWord. New word conversion can handle pdf too. If this would help, you can add *.pdf to office filters to use it automatically. In future CompareIt will use this library itself if main would fail to handle the file.