I'm assuming before the system only had the HDD and none of the User directory folders were changed from their default settings, and that there is practically no diff between the SSD partition and the HDD one.
If that's the case, I would try redoing the cloning operation, but following these steps:
- On the SSD, create a 200MB NTFS partition with the label S:\
- Mark the SSD as "Active" (either using DISKPART or Control Panel -> Administrative Tools -> Computer Management -> Storage)
- Clone the Windows partition into the SSD
- Open a command prompt as an administrator
- Execute the following command:
Bcdboot D:\Windows /s S:
This is assuming D:\Windows is the Windows partition on the SSD.
- Boot from the SSD.