Ok...took the time to create a video of how the programming of this Atmega328U-TH is behaving.
I did this so as NOT to be just another post on a forum where some other poor person has the same issue only to find there is no solution...yet.This is something just about every forum on earth rarely does...and that is to end with something useful 
And the fact that when the next person Google searches a Atmega328U-TH,they will most likely find this thread because nowhere is anything else about this thing.
Here is the Atmega328U-TH when I try to program it using routine procedures -
And here is an older video of how it is supposed to work and has many times using ANY of the Atmega328P-PU or 328P-AU.
And by the way...see the comment on the second video...he says the video is too fast to see what is going on.
This is a person that does not realize the "PAUSE" option on YouTube but yet wants to program an Atmega chip?
Gotta love the internet!
Jim