Odd, I have never seen that problem with sfc from the program before. Also SetAcl has been replaced in my Windows Repair starting with v3.5.0
I also notice in your screen shot that it is showing the cmd path is in the syswow64 folder. Normally the folder path of there the program is running would show there, even then when I check the cmd.exe in the task manager it is the cmd.exe from system32 that is running and not syswow64.
What version of Windows are you on?
My program isnt doing anything special, it makes the bat file with the sfc call and then is ran by the ShellExecuteW API. I just tried it on my Windows 7 system and do get any of the errors you mentioned.
Shane