What commands does Windows Startup Repair run?
Solution 1:
One thing you can do is click on the link that says "Click here for diagnostic and repair details", just before you are being asked to restart the system, so that the repairs are done.
This will show you a log of the changes/repairs done, depending on the problems that were found. The things done by startup repair vary depending on your actual problems.
In the image below you can see an example of a problem found by Startup Repair.
Solution 2:
Every time you apply a wim image(with imagex tool) to a disk or partition you must add boot entries(Windows BCD entries) manually. To do this, you should boot the computer with a WinPE disk and run the following command on the partition that you applied the wim:
bcdboot X:\Windows
where X is the unit that you applied the image. You are able to see what is the X value by running:
diskpart list volume