If you haven't already, check the contacts on the lens and camera to make sure they are clean. I have heard of no autofocusing problems with the G2 version of this lens, and even the first version, which I own, focuses very well and only
very occasionally refuses to focus.
You said that your 55-200 was not focusing properly, but now is. It's possible that there is an in camera issue. Try a rocket blower with the mirror down to clean dust out. The autofocus sensor can get goofy if there is a dust bunny on it.
Focus at longer distances can be tricky, too. Heat shimmer, humidity, and haze can all affect focus sharpness. Also, trying to achieve focus on a small object at a long distance is pretty tricky. Finally, remember that camera shake can greatly affect sharpness, especially when you've got the long, heavy lens all the way out to 600.
BTW, I don't think Nikon is specifically trying to handicap third party lenses. Tamron, Sigma, etc. are reverse engineering lenses, and so problems can naturally occur as a result. Since there have been no reports that I am aware of about the G2 150-600 failing to autofocus on Nikons, I don't think that is a concern at all. Tamron is making some great lenses these days, I hope you can get this sorted out!