"New And Improved", When It Ain't:

I've had an education.
You might need one too. This post is about internal combustion.
If you have no interest about what gets you to work or the grocery, skip this one.

Review:
Our Yamaha Super Tenere has now been at the dealership for repair almost two months.
One morning it would not start. We had it transported to the dealership where we bought it new and told them to "make it run".
We've love the bike. We've had a good relationship with the service the dealer has provided, (routine stuff like tire replacement, although the cost of same has been $omewhat eye-opening.)
But this event has been nothing short of extraordinary. 
I really feel at this point that they're searching for a needle in a haystack.
They can't get the bike to run.

The intake valves had obvious, SERIOUS carbon deposits. After breaking the engine down they got after those deposits like a Dentist attacking plaque on your teeth and removed them. They re-assembled the engine.
It still wouldn't start.

Much head scratching followed.
They actually had commented how clean the engine internals looked. We've paid "religious" attention to changing the oil and filter.
Only the valves look funky.

This is a "direct injection" gasoline engine, meaning the fuel is introduced directly into the combustion chamber. Fuel DOES NOT pass by the intake valves on the way to being burned.
So no amount of "Sea Foam" or "Chevron Techron" or "BG44" will improve this situation because none of that stuff will touch the intake valves. It CANNOT clean them. In the pursuit of improved fuel efficiency we may now be facing ugly "unintended consequences"...
Carbon buildup on intake valves, starting at about the 30,000 mile mark.

I'm now worried about our Taurus SHO, the engine in which has a similar design to the Yamaha, and seems to suffer a similar fate according to forums on that "Ecoboost" engine.
(And adding chemicals to the fuel to attempt to remedy the problem there overheats the turbochargers causing them to fail... $$$$$.)

This situation has a lot of people baffled.
And it makes carburetors look like wonderful, "Old Faithful" devices.

Any helpful comments would be GREATLY appreciated!
I'm sure experts would be grateful.