This makes me wonder whether there might be another setting needing adjusting in BIOS or something.
I have just taken a complete image of the machine as it now is, and may run Startup Repair, and see if that resolves the issues.
Value any other suggestions.
I would request you to go ahead and do a complete operating system reinstallation. There should be an issue with cloning since Os its taking time to load. Please reply with your findings.