Computer boots up into 'startup repair' after running disk cleanup
I just encountered the exact same problem, tried everything, didn't find a way to fix this either, had to restore from yesterday's backup, which does allow me to get the system back up and running.
I suspect this problem may be related to the fact that I'm using Dynamic Disk partitions on the disk Windows is installed. The problem has nothing to do with disk error, it's pretty clear Disk Cleanup deleted something important from Windows installation.