The File Integrity scan on my main site has previously run without problem. Now it takes several minutes to start and then hangs half way. When I go back there's a message that the last file took longer than 3 hours and I need to initialize data, which I do but it still doesn't complete the scan.
There are several subdomains that are listed in Exceptions. The Malware scanner and File Manager run well and skip the subdomains.
Open the log file when the scan freezes (there is a button to do that in the file integrity screen) and look for the latest file scanned.
For some reason the file integrity fails on it. You can try adding it as exception.