Hello, my name is Dan.
I will do my best to help you, the only stupid question is the unasked one.
I would suggest to you: Do not clone it, the problem is obviously in the user account and not hardware related. You have proven that by stating it came with the cloning.
Start fresh with a blank OS, install all applications and only restore data. Leave all System Preferences and settings behind, this will leave the problem behind also.
I had to do this on my iMac, not an upgrade but my main machine, developed an issue similar to yours. The only fix was all new installation of everything but data.
iTunes, movies, photos, documents and whatnot all restored group by group.
Still finding things I missed but no more problem.
There it is, not the easy answer you wanted but an answer that is correct and that will work.