As per the issue description mentioned above, you are facing issue when comparing files in Acrobat, is that correct?
Could you let us know dot version of Acrobat and the operating system installed on the machine? You may refer to the steps given in this link on how to check the version in Acrobat: Identify the product and its version for Acrobat and Reader DC
Does this happen with specific files? Have you tried with other pdf files?
Let us know if you need any help.