so a few questions have you tried running in safemode with networking? (stops most 3rd party programs from killing the repairs from running)
at any point during the repairs did you ever re open and close windows repair? (if you do this it will tell the program to close and thus the repairs will not complete even though it says it's running)
have you done a chkdsk /f /r (you may have data in bad sectors Possible hdd failure)
there can be multiple reason's why this can happen let's go down the list and narrow it down.