Hopefully it is just antivirus or other security related issue, Also avoid ever installing games into a System related folder, it's best to try and avoid the System drive altogether and make a folder dedicate to games on another drive.
Just a thought, you could try using something else to check and verify the files. For example QuickSFV or MD5Checker or other.
They can scan each file in a folder and subfolder creating a hash for each of the files, then later you can use it to check if any of the files have changed or are missing.
Though keep in mind many games for various stupid reasons keep files scattered over the system, such as in Windows User Account folders (like My Documents etc) so you may want to check those files too if no changes are found in the game's folder itself.
If you do discover game files are being changed, you could then find the culprit for causing problems, and just backup the files and copy them back in to avoid doing the verify / repair every time.
Though keep in mind some files will and should change, for example files that store save game or settings data.