I no longer use Perfect Disk for boot-time System file defrag since Puran seems to work better and offers a Disk Check in the run options. You might want to try that.
I would not ignore SFC failing to run. Try running it from System Recovery Options
Command Line: SFC -SCANNOW Run in Command Prompt at Boot.
If this fails I would consider a Repair Install
. I would also not use the suspect software again, especially because there is better freeware now available to do all that it does.